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The results of a survey of the major pathological conditions encountered in an established breeding colony of common cotton-eared marmosets (Callithrix jacchus) is presented. 265 home-bred and 70 imported wild-caught marmosets were examined. A Heinz body haemolytic anaemia and skeletal muscle myopathy were the most common pathological findings and were considered to be a result of a complex nutritional deficiency involving vitamin E, selenium and protein. Inflammatory disease of the intestinal tract was also a major feature. Chronic colitis was particularly common in older marmosets. Pneumonia, otitis media, meningitis and brain abscesses were important pathological findings in home-bred marmosets and were commonly associated with bacterial infections, particularly Bordetella bronchiseptica and Klebsiella species. Trichospirura leptostoma within pancreatic ducts of wild-caught marmosets was the only significant parasitic disease encountered. Mycotic infections of the upper alimentary tract with Candida species were occasional findings in debilitated animals. No pathological features suggesting viral diseases were found.