Paratuberculosis is mainly an infectious disease of ruminants with worldwide distribution. Infection occurs in early stages of life. Other animal species beyond ruminants are rarely affected, however, experimental and natural infections are possible. A case of paratuberculosis in a miniature donkey (Equus asinus f. asinus) with typical clinical and pathomorphological changes is reported here. Lesions were mainly observed in the intestine. Causative for the profuse diarrhoea with emaciation was massive diffuse granulomatous enteritis involving large quantities of acid-fast organism mainly in macrophages. Granulomatous inflammation with acid-fast bacilli again in macrophages to a lesser degree could be detected in the liver. Mycobacterium avium subsp. paratuberculosis (MAP) was isolated from intestinal contents after an incubation period of four weeks. MAP-specific DNA (IS900 and f57) was detected by polymerase chain reaction in culture material. Additionally MAP-isolates were characterized by multi-target genotyping (MIRU-VNTR- and MLSSR-typing). Isolates belonged to the Type II group and exhibited a unique genotype different from other MAP strains in Germany. The donkey originated from a donkey breeding farm in France with intensive free ranging cattle in the neighbourhood and could have been infected there. Donkeys should be considered as paratuberculosis-susceptible animals in exceptional cases and as possible reservoirs or disseminators of infection.