On January 9, 2013, the USDA published the new Final Rules in the Federal Register regarding Traceability for Livestock Moving Interstate. The new rule applies to horses moving interstate as well as to and from Indian reservations. The new system requires that horses be individually identified and accompanied by an Interstate Certificate of Veterinary Inspection (ICVI).
The American Horse Council published an article summarizing the new rules, which can be viewed here. The Final Rule published in the Federal Register can be viewed here.
The USDA has published Fact Sheets and other materials about the new rules, among them:
A Guide for Identifying Horses and Other Equines
Animal Disease Traceability Q&A