Scrapie Eradication Program in New York: What Every Sheep and Goat Owner Must Know
July 18, 2026
If you raise sheep or goats in New York, the Scrapie Eradication Program is not optional — it is a mandatory framework that governs how you identify, move, record, and report your animals. Failing to comply can result in movement restrictions, quarantine actions, and loss of market access.
This guide walks you through every major component of the program as it applies to New York producers, from understanding the disease itself to earning Scrapie-Free Flock Certification. Whether you manage a small hobby flock or a commercial operation, the rules covered here apply to you.
What Is Scrapie and Why It Is Regulated in New York
Scrapie is a fatal, degenerative disease that affects the central nervous system of sheep and goats. It is classified as a transmissible spongiform encephalopathy (TSE). You may recognize the TSE category from other well-known diseases — mad cow disease, or bovine spongiform encephalopathy, is probably the most familiar prion disease in the same family.
Scrapie is caused by a transmissible prion or abnormal protein which is very stable in the environment. This environmental stability is one of the key reasons the disease is so difficult to eliminate and why regulatory oversight is essential.
Scrapie is difficult to detect. It can take 2 to 5 years for an animal to show signs of disease, and current diagnostic tests require brain or lymphoid tissue. Animals typically live 1 to 6 months after they begin to show signs. Most are infected as young lambs or kids, but adult animals can get it, too.
Infected flocks typically experience significant production losses. 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. New York producers are directly affected by these trade and economic consequences, which is why state-level enforcement of federal scrapie regulations matters to your bottom line.
Common clinical signs include signs of central nervous system problems, most commonly incoordination or poor muscle control (ataxia), as well as weakness of any kind, including stumbling, falling down, or having difficulty rising. If you observe these signs in any animal 18 months of age or older, you are required to report the suspect animal to state and federal authorities.
New York’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. New York participates as a partner state within this framework, with the New York State Department of Agriculture and Markets (NYSDAM) serving as the primary state-level enforcement agency.
The National Scrapie Eradication Program has two major components: a regulatory eradication program called the Accelerated Scrapie Eradication Program (ASEP) and a voluntary certification program called the Scrapie Flock Certification Program (SFCP). As a New York producer, both components affect how you manage your flock.
To date, the program has eliminated scrapie in 99 percent of U.S. sheep and goats. However, the work is not finished. The United States is nearing the goal line after a 70-year battle against scrapie, a fatal disease that affects the brain of sheep and goats. While the current program has been very successful in drastically reducing the amount of scrapie in the U.S., we are still finding scrapie-positive animals.
The program’s goals are to eradicate classical scrapie from the United States and to meet World Organization for Animal Health (OIE) criteria for disease freedom. Your participation in New York’s scrapie program — through proper identification, recordkeeping, and reporting — directly contributes to achieving that national goal. You can learn more about the full scope of the program at the USDA APHIS National Scrapie Eradication Program page.
New York also offers a voluntary Sheep and Goat Health Assurance Program, coordinated with Cornell University, which helps owners develop farm-specific herd health plans to prevent disease outbreaks beyond scrapie alone.
Official Animal Identification Requirements in New York
New York State requires official scrapie identification on all sheep and goats upon change of ownership, unless they are sold directly to slaughter. There is no exception for younger animals. This is a stricter standard than the federal baseline, and it applies to every producer in the state regardless of flock size.
This identification can be approved scrapie eartags, registry tattoos, flock/individual ID tattoos, or any other approved federal scrapie identification. Understanding which form of ID is appropriate for each situation is critical, because the rules differ depending on how and where you are selling or moving your animals.
Approved Identification Methods
- Official Eartags (AIN Tags): For sheep and goats, AIN tags come with and without RFID capability. Your AIN tags that you order are uniquely linked to your own flock. You may not share them with another flock or herd. For animals born in New York, the state code on the tag is “NY”.
- Scrapie Flock ID Tattoos: Scrapie Flock ID tattoos can be used as official identification in both registered and unregistered sheep and goats. Your animal needs a Scrapie Flock identification number tattoo and a unique individual identification tattoo to be officially identified. Tattoos are official for moving your animals between farms, including interstate movements. Tattoos are NOT official for selling your sheep or goats in general auction sales. Your animals need an official eartag at those sales.
- Registry Tattoos: 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.
- Microchips: For microchips in your registered sheep and goats to be official, your breed registry must be accepted by the National Scrapie Eradication Program. Microchips are official for movements between farms, including interstate movements. Microchips are NOT official for general auction sales, and animals need an official eartag at those sales. There is no exception for animals sold slaughter-only.
Slaughter-Only Tags
A blue slaughter-only scrapie ID is only official for movement direct to slaughter. Animals with blue tags should not be found on farms and are not allowed at fairs, as these events are not in the slaughter chain. These animals must be processed within six days of entering New York State per New York state regulation.
Flock Registration and Recordkeeping Requirements in New York
Before you can obtain official identification tags in New York, you must have a flock ID or premises ID number assigned to your operation. A flock or premises ID is required to order tags from approved manufacturers. A national premises ID is also required to purchase official 840 RFID tags or implantable devices.
Recordkeeping is not just a best practice — it is a legal requirement under the scrapie program. The success of the Scrapie Eradication Program is tied to producers keeping good records of animal sales and purchases.
What You Must Record
Owners must keep a record of all scrapie tags, tattoos, and microchips that you put into sheep or goats. When you buy or sell an animal, you also need to record information about that purchase or sale. For sheep and goats, you need to keep that record for five years after you sell your animal.
Your records should include the official ID number of each animal, the date the ID was applied, the premises or flock of origin, the date and details of any sale or transfer, and the name and address of the buyer or seller. NYSDAM provides a template for recording eartags applied at your farm, available through the New York State Sheep and Goats Identification page.
Tag Portability and Flock Changes
If you move, all official ID should move with you, as they are associated with your flock rather than your physical location. If you move between states, your Flock ID will change and these tags will no longer be associated with the correct flock in the USDA database. Notify APHIS promptly if you relocate or dissolve your flock to ensure the national scrapie database remains accurate. For wildlife that may interact with your livestock in New York, you can explore resources on types of snakes in New York and other local species through Animal of Things.
Interstate and Intrastate Movement Rules for Sheep and Goats in New York
Movement rules are among the most consequential compliance areas for New York sheep and goat producers. Whether you are bringing animals into the state, shipping them out, or moving them to a local fair, specific documentation and identification requirements apply in every scenario.
Importing Sheep and Goats Into New York
The requirements for importing sheep and goats into New York State include a Certificate of Veterinary Inspection (CVI) issued by an accredited veterinarian. Each animal must be identified by a USDA approved scrapie ear tag or legible USDA assigned flock ID tattoo. Legible official registry tattoos that have been recorded in a sheep or goat industry association’s book of record may be used as official identification on the CVI when the animal is accompanied by a registration certificate.
There is no permit number required for importation into New York State. However, all additional man-made identification must be recorded on the CVI.
If your animals are destined for New York City, additional rules apply. Animals whose destination is within New York City may be subject to New York City Department of Health and Mental Hygiene regulations. Sheep and goats entering New York City for any reason must meet these regulations.
Moving Animals to Slaughter
Livestock moved into New York for immediate slaughter must be slaughtered within six days (144 hours). Animals in the slaughter chain must carry appropriate identification and may not be diverted to non-slaughter channels once they enter the state under slaughter-only status.
Intrastate Movements and Change of Ownership
The 2001 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. New York enforces this requirement, meaning any transfer of ownership within the state also triggers the ID requirement — not just movements across state lines.
Moving Animals to Fairs and Exhibitions
If you plan to exhibit sheep or goats at a New York county fair or the Great New York State Fair, additional health documentation is required. All goats must be identified by one of the following: USDA approved tags, a legible USDA approved registration tattoo, a legible USDA approved herd tattoo and individual animal ID number, or an electronic implant device (microchip) if the goat is enrolled in the Scrapie Flock Certification Program and/or the electronic implant ID is recorded on the goat’s registration paper.
For out-of-state animals attending New York fairs, the interstate CVI is valid for 30 days from the date of CVI inspection. During the fair season, from July 1 through Labor Day, interstate CVIs can be used multiple times as long as the initial entrance to a NY fair is within 30 days of CVI inspection and the CVI is initialed by a NYS Agriculture and Markets official at the fair.
Reporting, Testing, and Quarantine Requirements in New York
New York’s status as a Consistent State under the federal scrapie framework means the state is obligated to enforce active reporting, investigation, and quarantine procedures. As a producer, you play a direct role in this surveillance system.
When You Must Report
The accreditation standards require reporting of live or dead scrapie suspects to State and Federal authorities. If you observe an animal showing neurological signs consistent with scrapie — particularly in sheep or goats 18 months of age or older — you must contact your accredited veterinarian and NYSDAM immediately. Do not wait for the animal to die before reporting.
Infected sheep are identified through active slaughter surveillance, reporting of suspect animals by producers and accredited veterinarians, testing of mature sheep or goats that die on farm or at other locations, and live-animal testing of higher-risk animals. Your on-farm reports of dead or euthanized animals are a critical part of this surveillance network.
Sample Submission for Testing
APHIS provides shipping boxes and pre-printed, postage-paid labels at no cost to producers and accredited veterinarians. APHIS will pay for scrapie testing of up to 30 animals per flock per year. This means testing is effectively free for most New York producers. Producers may remove and submit whole heads or report deceased sheep or goats and ask for help with submitting samples.
The national annual sampling target is significant. The annual sampling goal set for the U.S. is 40,000 samples collected from sheep and goats 18 months of age or older to help find the final cases of scrapie and stamp out this disease. New York’s contribution to that target depends on producers and veterinarians submitting samples from animals that die or are euthanized on-farm. You can find your state’s designated scrapie epidemiologist (DSE) and local point of contact through the APHIS scrapie contacts directory.
Quarantine Procedures
When a flock is designated as infected or a source flock, state and federal authorities will place it under quarantine. If scrapie develops in a flock, the risk of further spread, reintroduction of the disease, or both can be minimized through removal of genetically susceptible exposed sheep and exposed goats, and if all susceptible exposed animals are not removed, live-animal testing and removal of test-positive animals.
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; genetic testing of sheep for scrapie susceptibility; and additional support measures. Quarantined flocks are also subject to post-exposure monitoring requirements. Flock owners that maintain a flock after receiving indemnity must maintain that flock under a post-exposure management and monitoring plan for 5 years. Five years of monitoring is consistent with normal epidemiological practice.
New York producers raising other animals alongside their sheep and goats may also find it useful to review resources on other wildlife in New York that could interact with livestock on your property.
Scrapie Free Flock Certification Program (SFCP) in New York
The National Scrapie-Free Flock Certification Program (SFCP) increases the marketability of sheep and goats from flocks that have demonstrated freedom of scrapie disease by adhering to program standards established by USDA APHIS. Enrollment is voluntary, but the benefits — especially for producers who sell breeding stock or export animals — are substantial.
Program Structure and Categories
The SFCP is a voluntary program that is open to all sheep and goat producers in the United States. 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 table below summarizes the key differences between these categories:
| Category | Status Options | Primary Goal | Best For |
|---|---|---|---|
| Export | Export Monitored, Export Certified | Certify flock as scrapie-free through annual inspections and strict sourcing rules | Producers selling breeding stock internationally or to high-value domestic buyers |
| Select | Select Monitored | Minimize scrapie risk through monitoring with fewer restrictions than Export | Producers seeking domestic market advantages without full export certification |
Export Category Requirements
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.
The SFCP identifies scrapie-free flocks by monitoring them over a 5 to 7 year period. This timeline reflects the long incubation period of the disease and ensures that any latent infections would have become detectable before certification is granted. The program provides sheep and goat producers the opportunity to increase the marketability of their animals through demonstrating a negligible scrapie risk in their flock or herd.
How to Enroll in the SFCP in New York
To enroll your New York flock in the SFCP, contact USDA APHIS directly at [email protected] or call 1-866-USDA-TAG (1-866-873-2824). All requirements of the SFCP are outlined in the SFCP program standards, available in electronic form through the USDA APHIS Scrapie Free Flock Certification Program page.
Accredited veterinarians are the producers’ primary source of education about all aspects of the program, including identification, recordkeeping, and movement requirements. Work closely with your accredited veterinarian to ensure your flock meets all enrollment prerequisites before submitting your application. SFCP tags may only be purchased by owners of flocks participating in the Scrapie-Free Flock Certification Program.
Once enrolled, your flock will be subject to annual inspections, ongoing recordkeeping audits, and required sample submissions. Maintaining your certification requires consistent compliance year over year — not just at the time of initial enrollment. For more information on raising animals responsibly in New York, explore guides on types of owls in New York and other native species that share the agricultural landscape with your flock through types of hawks in New York.
The American Sheep Industry Association also maintains a dedicated scrapie resources page with producer-focused guidance on identification and disease traceability systems that complements the official USDA materials.