The success of infertility treatment depends on the underlying cause and severity of the infertility problem. The current report addresses the complex genotype-phenotype interactions in an azoospermic man. Cytogenetic, molecular cytogenetic and molecular genetic studies indicated the derivative monocentric Y chromosome with duplication of Yp11 (including SRY gene) and partial deletion of Yq11 (including azoospermia factor - AZFb-c regions) as the most probable cause of the severe testicular failure. Our study emphasizes the importance of detailed genetic analysis in male infertility evaluation and helps to estimate the outcome of infertility treatment.