The gross and microscopic pathology of alkaptonuric ochronosis is presented from a study of pathologic specimens from six cases in our files and from a review of the literature. Emphasis is placed on the most clinically relevant organ systems involved by ochronosis: musculoskeletal, cardiovascular, genitourinary, eye, and skin. Recent electron microscopic discoveries from several affected organs, including the synovium, articular cartilage, cardiovascular system, eye, and skin, are included in this report. In addition, the molecular pathology of alkaptonuria is briefly discussed. The pathologic literature regarding alkaptonurin ochronosis is fragmented, as most cases of this rare entity are reported individually or as small series of cases. A comprehensive review of alkaptonuria has not appeared since the clinicopathologic review of the world literature by O'Brien et al in 1963. The purpose of this report is to present an updated and unified pathologic study of alkaptonuric ochronosis.