Male infertility affects a large proportion of the population. In spite of the magnitude of the problem and the considerable research effort that has been made to understand its causes, a large proportion of male infertility cases remain idiopathic in nature. This pilot genome-wide association study employed genotyping microarray technology to interrogate over 370,000 single-nucleotide polymorphisms (SNPs) in men with azoospermia and severe oligozoospermia, along with normozoospermic controls, in an effort to discover novel genetic variants significantly associated with male infertility. We found 20 SNPs significantly associated with azoospermia or oligozoospermia (P value for association of <1 x 10(-5)). Using a gene-centric approach evaluating SNPs associated with genes of known fertility function, we found 1 additional SNP with P < 1 x 10(-4). Although additional studies with larger numbers of samples will be required to validate these results and to identify causal variants, this study represents an important first step in applying genome-wide approaches to identify the genetic causes of male infertility.