We are reporting a 37 year old male with severe oligozoospermia and a history of infertility for thirteen years and surgery for severe unilateral varicocele. The hormonal levels for FSH, LH and T, and karyotype were within the normal range. Multiplex PCR revealed the presence of a de novo microdeletion in the azoospermia factor (AZF) c region involving the deleted in azoospermia (DAZ) and basic protein Y-2 (BPY2) genes. These results suggest that severe oligozoospermia should be considered for the screening of microdeletions of Yq involving the AZFc region even in the presence of a varicocele.