Testis specific protein (TSPY) is a human Y-chromosome derived gene with numerous functional and non-functional copies. Specific expression patterns in testis and testicular tumors, as in prostate cancer samples and cell lines led to the postulation of a potential role in cell proliferation, supported by the presence of a suppressor of variegation, enhancer of zeste and Trithorax/nucleosome assembling protein (nucleosome assembly protein) domain in the mature protein. Expression studies have now identified two transcripts of variable length, termed TSPY-S and -L, which differ in their 3′-translated region due to alternative splicing, and in the quantitative level of transcripts, with TSPY-S being at least 3–4-fold more abundant. In immunoblot experiments on human testis and LNCaP protein extracts using an anti-peptide-antiserum against the TSPY-L specific C-terminus TSPY-L was characterized as a functional variant on the protein level. As there are at least three intragenic positions differing between various TSPY genes and thus defining certain haplotypes, the alternatively spliced TSPY transcripts were analysed for their haplotypes in order to link them to well defined TSPY loci. Surprisingly, no evidence of a G-G-18 haplotype was found for the TSPY-L transcript, while this haplotype makes up almost 50% of all TSPY-S transcripts. This excludes the corresponding TSPY-1 locus from alternative splicing. The only significant differences between the TSPY-1 locus and eight other loci were identified in the promotor region as revealed by detailed sequence comparisons. Thus one might speculate that the alternative splicing could be influenced by elements binding to the promotor region.