Besnoitiosis is an emerging parasitic disease of equids. Italy is one of the few European countries where the circulation of Besnoitia spp. antibodies was demonstrated. In this study, a case of clinical besnoitiosis in two donkeys in northern Italy is reported. The two animals were clinically examined. Serum and blood samples were analyzed for the detection of Besnoitia spp. antibodies and for hematology, biochemistry, and enzyme activity, respectively. ITS-1 PCR and sequencing were carried out on DNA extracted from skin biopsies. Clinical examination revealed numerous scleral pearls in eyes of both animals; alopecia and hyperkeratosis with skin nodules in the region of the neck, hind leg, and on the pinnae were detected. No cysts were evidenced by endoscopy in respiratory and genital tracts. Both animals resulted seropositive to Besnoitia spp. antibodies by Western Blot. Hematology evidenced light anemia, leukocytosis with eosinophilia, and lymphocytosis; biochemistry and enzyme activity revealed hypoalbuminemia with decreased albumin/globulin ratio and elevated alkaline phosphatase values. Parasitic DNA extracted from skin biopsies of both donkeys demonstrated a homology of 100% with Besnoitia spp. This first clinical case of besnoitiosis in two donkeys in Italy both confirms the circulation of Besnoitia spp. in Italian equids and demonstrates that the distribution area of equine besnoitiosis in Europe could be wider than expected. Further studies are needed to infer its relevance, in relation to seroprevalence and clinical disease, and to identify the species of Besnoitia infecting donkeys. Besnoitiosis may be a neglected disease of donkeys in Europe: an early and accurate diagnosis is fundamental to implement adequate control measures to prevent a “silent” spread of Besnoitia spp. infection in equids populations.