A 3-year-old German shepherd dog was presented with a history of lifelong episodic diarrhoea. An adverse reaction to food was considered the most likely cause of the diarrhoea. The dog had received prolonged antibiotic therapy for most of its life as well as receiving probiotics containing the yeast Saccharomyces cerevisiae (syn. S. boulardi) for a year before referral. The probiotic was discontinued 2 months before to referral. Examination and culture of faecal samples identified yeast-like organisms, S. cerevisiae and Candida famata. S. cerevisiae has been isolated from humans in association with predisposing conditions such as prolonged sojourns in hospital, immunosuppression, broad-spectrum antibiotic therapy and prosthetic devices, but is regarded as non-pathogenic in humans and is rarely associated with disease in animals. C. famata has been isolated from animals, humans and the environment, but is regarded as a very rare pathogen. No evidence of immunosuppression was found in the dog. The presence of yeasts in the faecal isolates and the history of prolonged use of antibiotics and probiotics with a concurrent adverse reaction to food, suggest that conditions may have occurred within the bowel that made it possible for the yeasts to colonise parts of it. This has apparently not been reported before.