Colorado Scrapie Eradication Program: Rules Every Sheep and Goat Owner Must Know

If you raise sheep or goats in Colorado, scrapie compliance is not optional — it is a legal requirement that affects every sale, movement, and ownership transfer you make. Failing to meet state and federal identification, recordkeeping, or movement rules can result in quarantine, restricted sales, and financial penalties that hit your operation hard.

This guide walks you through every layer of Colorado’s scrapie eradication framework: what the disease is, how the state participates in the national program, what identification your animals must carry, how to register your flock, what movement rules apply, and how voluntary certification can boost your marketability.

What Is Scrapie and Why It Is Regulated in Colorado

Scrapie is a difficult and devastating disease of sheep and goats classified as a transmissible spongiform encephalopathy (TSE), which affects the central nervous system and is always fatal. There is no treatment or cure, and the disease can silently devastate a flock before producers even realize it is present.

It can take 2 to 5 years for an animal to show signs of disease, and current diagnostic tests require brain or lymphoid tissue. Apparently healthy animals infected with the disease agent can spread it. This makes early detection and strict regulatory compliance your most effective lines of defense.

Most scientists believe that scrapie is caused by prions — an abnormal form of a normal cell protein. It appears to spread most commonly from an infected ewe to her offspring and other lambs that come in contact with the placenta and placental fluids. The environment can become contaminated and remain so for years, serving as a source of infection to susceptible animals long after these materials have been removed.

There are two types of scrapie: classical and nonclassical. Nonclassical scrapie is also referred to as atypical, Nor98, or Nor98-like scrapie. Nonclassical scrapie appears to occur sporadically and has occurred in sheep of all the common genotypes and goats. The regulatory program in Colorado, consistent with the national program, focuses on classical scrapie.

Scrapie is estimated to cost the U.S. sheep industry over $20 million a year and can potentially affect your flock. The U.S. sheep and goat industry continues to experience export losses and increased production and disposal costs because the United States is not free of scrapie. Regulation in Colorado is therefore both an animal health measure and an economic protection for producers statewide.

Common clinical signs you should watch for include gait abnormalities such as high stepping of the forelegs, hopping like a rabbit, and swaying of the hindquarters. Clinical signs of classical scrapie typically appear between 2 to 5 years after infection, so infected animals rarely show signs before age 2. Due to damage to the nervous system, affected animals often show behavior changes such as nervousness or aggression, intense rubbing, and locomotor incoordination that progresses to recumbency and death.

Colorado’s Role in the National Scrapie Eradication Program

The National Scrapie Eradication Program (NSEP), a cooperative State-Federal-industry program, is working to eradicate classical scrapie from the United States and meet World Organisation for Animal Health (WOAH) criteria for disease freedom. Colorado participates as a partner in this effort, aligning its state-level rules with federal standards.

The National Scrapie Eradication Program, coordinated by the U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS), has reduced the prevalence of scrapie in adult sheep sampled at slaughter by over 99 percent. Despite this progress, the program is conducting targeted sampling of subpopulations that have a higher prevalence of scrapie than the general sheep and goat population to find the remaining cases.

Colorado’s rule defines the requirements for importing breeding sheep and goats into the state, sets forth identification requirements for the transfer of ownership or the exhibition of sheep and goats, and establishes disease protocols for sheep and goat flocks infected with scrapie. This rule is necessary to bring Colorado’s standards into compliance with federal scrapie rules so that Colorado can be deemed a scrapie-compliant state.

This in turn affects Colorado’s ability to qualify for grants under various federal disease control programs and allows less stringent interstate movement. In other words, your compliance directly affects the economic opportunities available to every producer in the state.

APHIS published a final rule in the Federal Register in 2019, updating scrapie program regulations (9 CFR 79). The rule established a more flexible approach to disease investigations and affected flock management and more consistent animal identification and recordkeeping requirements for sheep and goats. Colorado’s regulations under 8 CCR 1201-16 track these federal standards.

Official Animal Identification Requirements in Colorado

In an effort to eradicate scrapie in the United States, USDA requires sheep and goats to have official flock identification ear tags that list their flock of origin. Enforcement of these rules is now in effect as the tags are readily available to producers.

The following animals are required to carry official USDA flock or herd ID tags:

• All sheep that are sexually intact, regardless of age; all wethers 18 months of age and older upon change of ownership; and all cull sheep 18 months or older moving to slaughter.
• All sheep sexually intact regardless of age for show or exhibition; all wethers 18 months of age and older for show or exhibition; and all breeding sheep regardless of age.
• All goats sexually intact regardless of age; all wethers 18 months of age and older upon change of ownership; all cull goats 18 months or older moving to slaughter; and all goats sexually intact regardless of age for show or exhibition.
• Due to scrapie found in goats in Colorado, all commercial goats sexually intact regardless of age and wethers 18 months of age and older not in slaughter channels must also carry official ID.

Official identification takes one of three forms under Colorado’s rules. Official identification includes: 1) ear tags and/or microchips approved by the USDA for scrapie identification; 2) registration tattoos in goats when accompanied by a matching certificate of registration from a goat breed registration association; or 3) an APHIS-assigned tattoo or tattoo for animals that cannot be ear-tagged.

Registered animals may be identified with a registration tattoo instead of a tag, as long as the animal is accompanied by a copy of the registration certificate issued by an APHIS-approved registry listing the current owner, or the registration certificate and a completed transfer of ownership form dated within 60 days that lists the current owner.

Producers should consider the different devices available — including metal or plastic tags, radio frequency identification (RFID) tags, and RFID implants (there are restrictions on the use of implants) — and choose what works best for them. Devices for use only on animals in slaughter channels must be medium blue and marked with the words “Meat” or “Slaughter Only.” Devices that use RFID must conform to ISO 11784 and ISO 11785 standards unless otherwise approved.

The preferred placement for eartags is in the left ear to aid in shearing. Official tags may not be sold or given to another person. If you no longer need the tags, they should be destroyed or returned to the APHIS Veterinary Services District Field Office.

Flock Registration and Recordkeeping Requirements in Colorado

Before you can obtain official identification tags, you must have a registered flock or premises ID. To obtain a flock or herd/premises ID, owners must contact the APHIS Area Veterinary Services at 1-866-USDA-TAG for a flock identification number. This number is the foundation of every other compliance requirement.

Flock ID tag numbers are the producer’s flock ID assigned by APHIS or the State, followed by an individual animal number. Metal serial tag numbers have the State postal abbreviation — two letters followed by four numbers. Keeping these numbers organized is essential for accurate recordkeeping.

Colorado producers who sell or dispose of sheep and goats must maintain detailed transaction records. Individuals who sell or dispose of sheep and goats should maintain records of the number of animals sold and disposed; the date of sale; the name, address, and phone number of the buyer or person who acquired the animals; and the flock of origin ID numbers.

Records on purchases must be maintained for five years of the number of animals sold and disposed; the date of sale; the name, address, and phone number of the buyer or person who acquired the animals; and the flocks of origin. This five-year retention rule applies to both purchases and sales.

Producers must also keep herd records showing what new animals were added and what animals left the herd or flock. These records are not just a bureaucratic formality — they are the traceability backbone that allows state and federal officials to contain a scrapie outbreak quickly if one occurs.

Interstate and Intrastate Movement Rules for Sheep and Goats in Colorado

Movement rules in Colorado apply whether you are bringing animals into the state, moving them across state lines, or transferring ownership within Colorado. The rules differ based on the type of animal, its intended use, and whether a change of ownership occurs.

In September 2001, the scrapie regulations were revised to require the official identification of sheep and goats not in slaughter channels (except low-risk commercial goats) and any sheep over 18 months of age in interstate commerce with some exceptions. In addition, the revision required States to implement and enforce official identification of most sheep and goats on change of ownership intrastate in order to move sheep and goats interstate with minimal restrictions.

For animals being imported into Colorado, the requirements are clear. Certificates of Veterinary Inspection (CVIs) for all breeding sheep and goats imported into Colorado must contain official identification for each animal. The CVI must also include a statement verifying that the livestock have been inspected and are free from clinical signs of any contagious, infectious, or communicable diseases and that the livestock do not originate from an area of quarantine, infestation, or infection. A certificate of veterinary inspection is valid for thirty days.

Sheep and goats imported from Canada or Mexico must have a permanent country mark and other official identification.

Colorado also recognizes a commuter permit for producers who operate across state lines. A commuter permit is issued to a producer who routinely uses land in Colorado and a contiguous state to allow movement of a breeding flock and its progeny between Colorado and the contiguous state without complying with the Colorado scrapie import requirements. The permit is valid for 12 months after the animal health officials of the contiguous state and the producer have signed the agreement application provided by the State Veterinarian.

There are limited exemptions from official ID requirements for intrastate movement. Sheep or goats moved for grazing or similar management reasons without a change of ownership when moved from a premises owned or leased by the owner to another premises owned or leased by the same owner are exempt. The premises must be recorded in the National Scrapie Database as additional flock premises, and commingling must not occur with unidentified animals born in another flock.

Animals moving in slaughter channels have a separate pathway. Sheep or goats moving in slaughter channels or direct to slaughter without official identification must have an Owner/Hauler Statement with group/lot identification, with an exception for wethers that are less than 18 months of age. Templates for the Owner/Hauler Statement are available on the Colorado Department of Agriculture and USDA websites. You can also review Colorado’s other animal regulation frameworks for broader context on how the state structures its livestock and animal rules.

Reporting, Testing, and Quarantine Requirements in Colorado

When scrapie is suspected or confirmed in a Colorado flock, a structured series of state and federal obligations takes effect immediately. Understanding these requirements before a problem arises is essential to managing an outbreak effectively.

Cull breeding sheep and goats destined for slaughter will be tested for scrapie. During the scrapie surveillance program, the ID tags will be collected to accompany the test sample and used to trace an animal that tests positive for scrapie back to its infected flock.

APHIS will pay for scrapie testing of up to 30 animals per flock per year. Producers may remove and submit whole heads or report deceased sheep or goats and ask for help with submitting samples. APHIS also provides shipping boxes and pre-printed, postage-paid labels at no cost to producers and accredited veterinarians.

Genetic classification plays a central role in Colorado’s quarantine and management protocols. Genetically susceptible animals include all goats and any sheep which tests QQ at Codon 171. A high-risk animal means any goat or genetically susceptible female sheep which is: the progeny of a scrapie-positive dam; born in the same flock during the same lambing season as progeny of a scrapie-positive dam; or a scrapie-susceptible animal that has been present in a flock and has been exposed to amniotic fluid of a scrapie-positive dam.

For infected flocks, Colorado’s rule outlines specific management strategies. The most promising strategy for the control and eradication of scrapie in sheep is the use of resistant genotype rams to assure that all progeny contain at least one resistant gene, regardless of the dam’s genotype. Using homozygous resistant rams in an infected or source flock will virtually eliminate scrapie transmission.

APHIS provides the following assistance to owners of exposed and infected flocks or herds that participate in cleanup plans: indemnity for high-risk, suspect, and scrapie-positive sheep and exposed goats that owners agree to destroy; and genetic testing of sheep for scrapie susceptibility.

Accredited veterinarians carry specific obligations under the program. The accreditation standards require reporting of live or dead scrapie suspects to state and federal authorities. In addition to this critical role, accredited veterinarians are the producers’ primary source of education about all aspects of the program, including identification, recordkeeping, and movement rules.

For genetic testing to be valid in regulatory activities, strict protocols apply. All genetic tests must be collected by an accredited veterinarian or State/Federal animal health official, must occur at a laboratory approved for such purposes by the USDA, must be submitted on forms approved by the USDA, and must be on animals identified with USDA-approved methods.

You can learn more about Colorado’s broader animal regulatory environment to understand how state oversight applies across different species and situations. For producers interested in understanding how wildlife interacts with livestock in Colorado, resources on native wildlife species in the state may also be relevant to biosecurity planning.

Scrapie Free Flock Certification Program (SFCP) in Colorado

Beyond baseline compliance, Colorado producers can voluntarily enroll in the Scrapie Free Flock Certification Program (SFCP) — a pathway that reduces your flock’s scrapie risk, improves animal marketability, and contributes to national eradication goals.

The Scrapie Free Flock Certification Program was established in 1992 through the combined efforts of APHIS, the States, and the sheep and goat industries. The SFCP is a voluntary program for sheep and goat flock owners who wish to reduce or eliminate the risk of introducing classical scrapie into their flocks.

The overall objective of the SFCP is to minimize the scrapie risk of participating flocks and herds, thereby improving the marketability of animals from participating flocks and herds and contributing to the national scrapie eradication program. The SFCP has two categories: Export and Select. The Export category has two statuses — Export Monitored and Export Certified — and the Select category has one status: Select Monitored.

The two categories differ significantly in their requirements and the benefits they provide:

The objective of the Select category is to enhance scrapie surveillance by increasing the reporting of animals with clinical signs of scrapie and submission of samples for scrapie testing. Select flocks are required to submit samples from at least one mature animal for scrapie testing every 1–3 years, depending on the size of the flock or herd. Participating flocks do not advance to a certified status.

The objective of the Export category is to certify participating flocks and herds as scrapie-free establishments through limiting the acquisition of does and ewes from flocks of the same or higher status, annual inspections including reconciliation of the animal inventory, official individual animal identification requirements, recordkeeping requirements, and animal sampling requirements.

Export Certified animals from these flocks meet the World Organization for Animal Health’s standards to be recognized as free of disease. In order to achieve Export Certified status, a flock must gain a minimum of seven years in status and sample 30 mature animals. This sampling minimum may be achieved through slaughter, necropsy, and live animal testing.

Enrollment in the SFCP requires completing VS Form 5-22 and submitting it to your APHIS Veterinary Services area office. The State Scrapie Flock Certification Board or its representative reviews applications and approves admissions to the program. You can enroll at the USDA SFCP online portal.

Once enrolled, participants take on specific ongoing obligations. Flock owners who join the SFCP commit to monitoring their flocks for evidence of scrapie and reporting all clinically suspect animals to APHIS or State authorities for testing. Monitoring includes individual animal identification, accurate recordkeeping, observation and evaluation of animals for clinical signs of scrapie (including death), and testing a specified number of test-eligible animals.

Participants must notify the State Scrapie Certification Board and/or the Veterinary Services Area Office within 30 days of any action resulting in a change in status or status date, such as the acquisition of or commingling with nonparticipating animals or embryos, animals or embryos with a lower status or status date, or use of sheep or goat milk, colostrum, or products derived therefrom.

Whether you are a small hobby farm owner or a large commercial operation, understanding and following Colorado’s scrapie eradication requirements protects your animals, your neighbors’ flocks, and the long-term viability of the state’s sheep and goat industry. Start by calling 1-866-USDA-TAG to register your flock, then review the Colorado Department of Agriculture’s official scrapie rule (8 CCR 1201-16) for the complete regulatory text. For additional context on Colorado’s animal and wildlife landscape, explore resources on native owl species in Colorado, hawks found across the state, and other raptors that share Colorado’s agricultural landscape.