© 2016, © The Author(s) 2016. Objectives: Our objective was to perform the first multicentric study in Spain to evaluate the prevalence of feline herpesvirus-1 (FHV-1), feline calicivirus (FCV), Chlamydophila felis and Mycoplasma felis in cats with upper respiratory tract disease (URTD), conjunctivitis and/or gingivostomatitis (GS) compared with control cats; and to evaluate risk factors for these clinical conditions. Methods: Conjunctival and oropharyngeal swabs were collected and a questionnaire regarding signalment, lifestyle, vaccination history and clinical signs was obtained for each cat. Swabs were tested for each pathogen by real-time PCR. Results: The study population consisted of 358 cats, including 98 control cats. Among the 260 diseased cats, 127 cats presented with URTD, 149 cats had conjunctivitis, 154 cats were suffering GS; many cats presented more than one clinical condition. The prevalence observed of FHV-1, FCV, C felis and M felis was, respectively, 28.3%, 48.0%, 20.5% and 46.5% in cats with URTD; 24.2%, 43.6%, 19.5% and 38.3% in cats with conjunctivitis; and 15.6%, 58.4%, 9.1% and 37.7% in cats with GS. Prevalences in the control group were 6.1%, 15.3%, 2.0% and 20.4%, respectively. Coinfections were common among all groups of cats. Risk factors were identified for all groups. FHV-1, FCV and C felis were associated with URTD and conjunctivitis. FCV was strongly associated with GS. M felis was present in a high percentage of the population in all groups, but its role in these clinical conditions remains uncertain. Vaccination was protective for URTD and GS but not for conjunctivitis. Conclusions and relevance: This epidemiological study describes, for the first time, prevalence for FHV-1, FCV, C felis and M felis in Spain. In general, the prevalences found are similar to those reported in other countries. Factors associated with disease expression were also identified, which are relevant for practitioners.