A 4-day-old male Martina Franca donkey foal was evaluated for a forelimb alteration. Clinical examination and radiographs revealed the agenesia of the distal digit. Biochemical parameters were normal, and ultrasonographic evaluation did not identify any relievable organ alteration. Karyotype study revealed an abnormality on chromosome 1. The foal was discharged with a distal limb bandage in which a palmar splint was applied. A poor prognosis for the functionality of the limb was given. In endangered species, such as the Martina Franca donkey, the excessive inbreeding could result in an increase in genetic disorders. These findings shed new light on the possible pathogenesis of the digital dysgenesia. The study of the karyotype could be a useful approach to detect genetic alterations that could or could not be expressed in the animal, especially in endangered species in which a risk of an excessive inbreeding is considerable. These defects should be considered in the choice and selection of the breeders.