The detailed analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions of the long arm of the human Y chromosome, termed AZFa, AZFb and AZFc, (AZF: AZoospermia Factor) that are currently deleted in men with otherwise unexplained spermatogenic failure. Screening for these deletions is now common in many infertility centres and in some instances they have a prognostic relevance. Recently, attention has turned to partial deletions of the AZFc region. At first sight some of these deletions appear to have little effect on fertility, whilst others appear to be associated with significant risk for developing spermatogenic failure. However, the relationship between these partial AZFc deletions, reduced sperm counts and infertility is the subject of a continuing intense debate. There is a pressing need to clarify the impact of partial AZFc deletions on human spermatogenesis. This requires large-scale studies on well-characterized normospermic and oligo/azoospermic individuals of different ethnic origins with multiple informative AZFc markers if the correlation between these deletions and the phenotype is finally to be resolved. The definition of Y chromosome variants (haplotypes) in cases of partial AZFc deletions is likely to play an essential role in understanding the contribution of the deletion to reduced sperm counts.