Alport Syndrome is a heritable progressive renal disease that, despite the large number of published studies, because of its genetic, clinical, immunohistochemical, and ultrastructural heterogeneity, still remains a diagnostic challenge. The focus of the discussion is on electron microscopy and immunohistochemistry Col (IV) chains. The differential diagnosis from thin glomerular basement membrane disease is discussed in depth, because both are familial, and can have similar clinical presentation and even ultrastructural pathology, but with a different outcome. The diagnostic role of molecular genetics, which identified the presence of collagen IV gene mutations and its relationship to the phenotypic expression of the renal damage, is also discussed.