Reproductive pathology is a challenging field that is not typically encountered in the routine diagnostic work conducted by most pathologists. Reaching a diagnosis can be difficult and is often a multifactorial process involving a team of people located on-farm and in laboratories. Diagnosis often requires evaluation of historic and current diagnostic information, gross and histopathological evaluation, and a suite of adjunct laboratory tests. The guidelines in this visual atlas have been developed to support diagnosis of currently recognised causes of equine reproductive loss and, potentially, the recognition of emerging diseases. The guidelines focus on the case definition, clinical features, additional testing and histopathological features of these diseases; the gross features and approach to necropsy are discussed in the Visual Atlas of Gross Pathology. Additional resources on normal histology and common pathological processes in foetal tissues and placental membranes, and histopathology templates and guidelines, are also provided.