A group of 22 unrelated patients with sporadic or non-X-llnked Alport syndrome were screened for mutations In the non-collagenous domain of the type IV collagen a3 (COL4A3) chain gene. The five 3’-exons of this gene, located on chromosome 2qter, were tested by single strand conformation polymorphism analysis and direct sequencing. One patient was heterozygous and another homozygous (Mochlzukl et a/., Nature Genetics, In press) for a deletion of five nucleotldes. A third patient appeared to be a compound heterozygote for two different nonsense mutations. In two patients and the father of a deceased patient we found a heterozygous substitution of an evolutionary conserved leuclne by proline. However, segregation data of the mutation and a COL4A3/COL4A4 CA-repeat marker In their families argued against a causative role of the mlssense mutation. Even drastic changes of strongly conserved amlno acids, as in the Leu36Pro case, may not be significant. Autosomal recessive inheritance due to pathogenic COL4A3 mutations accounts for at least 13% of Alport syndrome cases in this sample. It Is concluded that COL4A3 is a major gene in the genetically and clinically heterogeneous Alport syndrome.