Post-mortem examination is a key step in the diagnostic process of infectious diseases in sheep and goats. Diagnostic pathology deals with identification and study of lesions, at the same time providing also significant clues regarding pathogenesis of the diseases. This article reviews the salient pathological findings associated with the most significant infectious diseases of sheep and goats present in countries where small ruminants are a relevant agricultural industry. Lesions are reviewed according to the different organ systems where they occur. Emphasis has been given in the description of the salient lesional patterns than can be identified in each organ and which can be of help in the differential diagnosis of the lesions caused by bacteria, viruses, fungi or prions. Finally, a review of the usefulness of ancillary tests that may be used on various tissue samples for performing an aetiological diagnosis, is included; the application of various techniques, from immunohistochemistry to molecular biology-based tests, is described.