The evaluation of occurrence of Chlamydophila felis, cryptic plasmid, FHV-1 and its association with retroviruses is essential for optimal clinical approach in cats living in shelters. This study is aimed at determining the occurrence of C. felis by PCR in eye conjunctiva and oral swabs, FIV/FeLV in blood samples by ELISA in 186 cats from 3 catteries. The symptoms of animals were ranked from 1 (least) to 4 (worst). The best clinical and health management was observed in the first cattery, whose predominant stage of symptoms was 1 (59.32%), the second cattery was classified as intermediate and its animals were mostly in grade 3 (41.38%), the third cattery had poor sanitary structure and the animals were classified as grade 3 (66.67%). The observed occurrence of C. felis was 7.41% in the first cattery, 46.15% in the second and 23.08% in the third. Positive animals were subjected to PCR of three genes of the cryptic plasmid, but no correlation between the worst clinical conditions and the presence of this plasmid were found, so it wasn't considered a virulence factor. Since it needs 3 PCR reaction for its detection, the plasmid does not have diagnostic importance. In all animals in which C. felis was detected, FHV-1 was also present. Frequency of FIV/FeLV observed was low and not correlated with the mortality or morbidity of these shelters. We conclude that the frequency of C. felis observed was high in the shelters with the worst clinical and sanitary conditions.