Objectives: Otitis externa is seen clinically in cats, although studies investigating this condition within the UK are lacking. The objective of this study was to investigate the prevalence of Otodectes cynotis mites and microbial infection in the ear canals of cats in various rescue centres and a referral hospital. Methods: Otoscopy was performed in 332 cats. Otoscopic findings were noted, including the gross visualisation of Otodectes species. A sample of cerumen was collected for cytological evaluation and a cerumen smear for detection of Otodectes mites if there was a large amount of aural exudate present. Results: O cynotis infestation was noted in 3/341 cats (0.9%, 95% confidence interval [CI] 0.3–2.6). A total of 129/341 (37.8%; 95% CI 32.7–43.0) cats were found to have Malassezia species within one or both ears. Bacteria were found unilaterally in 9/341 (2.6%; 95% CI 1.4–4.9) cats. Analysis of the cytological findings showed an increased likelihood for Malassezia species to be present as age increased (n = 293; Pearson r = 0.204, P <0.001). There was also an increased likelihood of finding Malassezia species in both ears if found within one ear (n = 327; r = 0.499, P <0.001). There was a positive correlation between the number of Malassezia organisms and the quantity of aural exudate (n = 338; r = 0.778, P <0.001). Cats in which Otodectes species infestation were noted (n = 3) had moderate or large quantities of cerumen. Conclusions and relevance: This study shows that there was a low prevalence of O cynotis in this cohort of cats. In normal cats it was not unusual to find Malassezia microorganisms upon aural cytology, bacteria were noted far less frequently and in two cats this was associated with underlying anatomical pathology.