Although in the past decades much progress in testicular cancer (TC) management has been made, little is known about the possible genetic causes and molecular mechanisms involved in its aetiopathogenesis. Some studies on possible contribution of the Y chromosome in TC development have been previously published, but data are not conclusive. In particular, ethnic influence and spermatogenic activity of patients with TC have not been adequately considered in previous studies, although they may represent important confounding factors. The objective of this study is to analyse the contribution of the Y chromosome in testicular germ cell cancer subjects who are well defined at the microgeographical, clinical and seminological level. We analysed Y chromosome classic azoospermia factor (AZF) deletions, partial AZFc deletions and Y haplogroups in 118 sporadic cases of testicular germ cell cancer and 93 microgeographically matched controls. Y chromosome screening failed to identify Y chromosome microdeletions in either cases or controls. Y chromosome haplogroup distribution and frequencies did not differ between cases and controls. Furthermore, no difference was observed when comparing patients with seminoma and non-seminoma, nor when comparing patients with TC with normozoospermia and azoo-oligozoospermia. Our findings combined with data reported so far suggest that classic AZF deletions and partial AZFc deletions are not a frequent cause or risk factor for TC and that different Y haplogroup distribution does not contribute to susceptibility to this tumour.