In order to study the special composition of animals used in the medieval medicine of Azerbaijan, a wide range of medieval sources on medicine and pharmacognosy from the collection of the Institute of Manuscripts of the Azerbaijan Academy of Sciences in Baku has been studied. About 40 medieval sources from the 10-18th centuries including 17 manuscripts in Turkic, Persian and Arabic have been selected as the objects of this study. As a result, 150 species of animals described in medieval Azerbaijani books on medicine and pharmacy have been identified. Many of the identified animals are mammals, (47 species or 31% of total number of identified species). The medieval authors describe 12 species of reptiles and 4 species of Amphibians (frogs, toads, salamanders and tree-frogs (Hyla arborea). 15 species of fishes described in medieval manuscripts have been identified. The identified molluscs are cuttlefish (Sepia officinalis), mussel (Mytilus edulis), octopus (Octopus vulgaris) and snail (Helix pomatia). Most crustaceans used in medieval Azerbaijan medicine belong to Decopoda. Medieval manuscripts contain numerous names of various worms and insects (ants, flies, beetles, etc.), however their exact identification is rather difficult. As usual, medieval authors unite a number of species under one name and do not give sufficient information about their morphology. Results of the research create grounds for the idea that the recommendations of the medieval authors on the medicinal application of animals can be applied to modern medicine once they have been experimentally and clinically tested.