A reverse transcriptase polymerase chain reaction (PCR) was used to amplify a 235 bp hypervariable region of the feline calicivirus (FCV) genome which encodes part of the capsid protein. Sequence from this region was used to compare viruses used in three attenuated vaccines to viruses isolated from vaccinated cats with clinical signs of FCV-infection (vaccine failures). All three vaccine viruses contained sequence similar to that published for FCV strain F9 (Carter et al. 1992, Virology 190, 443-448). However, two of the three vaccines contained a separate sequence which was 20.67% distant (number of nucleotide substitutions per 100 bases) from F9. The sequences derived from isolates obtained from vaccine failures fell into two categories. Most were distinct (21.33-38.00% distant) from vaccine sequence. However, in some cases, sequences were sufficiently similar to the vaccines' (0.00-5.33% distant) to suggest that the isolate may have originated from the vaccine. In addition, comparison of sequence determined for isolates from the same disease outbreak showed them to be closely related (0.00-1.33% distant), whereas epidemiologically unrelated isolates were 20.67-38.00% distant.