Using cDNA microarray hybridization from a human testicular cDNA library, one gene exhibiting 6.4-fold difference at expression level between adult and embryo human testes was cloned and named tsIQGAP2 (testis specific IQ motif containing GTPase-activating protein 2). The full cDNA length of tsIQGAP2 is 3388 bp and contains a 3215 bp open reading frame, encoding a 122.85 kDa protein of 1071 amino acids. Sequence analysis showed that tsIQGAP2 harbors all the domains (one WW domain, three IQ motifs, and one RasGAP homology domain) in HsIQGAP2 (IQ motif containing GTPase-activating protein 2) except for the N-terminal calponin homology domain. Blasting human genome database localized tsIQGAP2 to human chromosome 5q13-14 and further investigation showed that it is a novel transcript variant of HsIQGAP2. The tissue distribution of tsIQGAP2 showed that it is a testis specific gene. The above results suggest the potential role of tsIQGAP2 during spermatogenesis and the mechanism by which tsIQGAP2 regulating spermatogenesis also has been proposed.