Alport syndrome (AS) is genetically heterogeneous. The gene COL4A5 is mutated in the more frequent X-linked dominant form of the disease whereas COL4A3 or COL4A4 are mutated in the autosomal recessive and dominant forms. Diagnosis of AS and determination of the mode of transmission are important because of the differences in prognosis and genetic counselling attached to these different forms. Recently, promising results have been obtained in Col4a3-null mice, an animal model for AS, with different therapeutic trials when administered early in the course of the disease, an additional reason for making early diagnosis of AS in children. Since the identification of the molecular basis of the disease, mutation screening is theoretically the best diagnostic approach, avoiding the use or renal or skin biopsy. However, for many reasons linked to the genetic heterogeneity of the disease, the large size of the three genes and the random distribution of the mutations all along these huge genes, this method is tedious, expensive and time consuming. Moreover, its sensitivity is reduced. For these reasons, evaluation of the expression of type IV collagen chains in the skin, and if necessary in the renal basement membrane, remains a useful tool for AS diagnosis. At this time, the indication for these different approaches, which are not mutually exclusive but complementary, depends on the patient clinical presentation and family history.