Two visits, six weeks apart, were made to a cat rescue shelter and single oropharyngeal swabs were taken from all the compliant cats. Feline calicivirus was isolated from 14 of 45 swabs (31 per cent) taken on the first visit and 12 of 46 swabs (26 per cent) taken on the second visit. Nucleotide sequences were obtained for nine isolates from the first visit, six isolates from the second visit, and for the vaccine virus used in the cattery. Distance analysis showed that the majority of the isolates could be assigned to one of two groups. All the isolates obtained from cats sharing the same pen or isolates obtained from the same cat on successive visits, were less than 5 per cent distant, whereas most of the isolates from cats in different pens were more than 20 per cent distant. Phylogenetic analysis showed that at least seven distinct field isolates were present in the cattery. The only good evidence for virus transmission within the cattery was a case in which two viruses isolated from cats in different pens had sequences that were less than 5 per cent distant.