Microphthalmia-associated transcription factor (MITF) is involved in white spotting and deafness associated with lack of pigmentation in human and mice. In the present study, we employed MITF-associated markers to evaluate MITF as a candidate for canine congenital sensorineural deafness (CCSD) in Dalmatian dogs. We performed an association study using MITF flanking and intragenic markers for 88 Dalmatian dogs of different hearing and eye pigmentation status. A significant association was identified for MITF-related markers with CCSD and blue iris colour. We conclude that MITF might play a role in CCSD and blue eye colour in Dalmatian dogs.