Survivin, a novel antiapoptosis gene, was identified as a member of the inhibitor of apoptosis protein (IAP) family. Unique among IAP, survivin has been found to be abundantly expressed in a wide variety of human malignancies, whereas it is undetectable in normal adult tissues. Recently, three splicing variants of survivin have been further characterized with different subcellular localization, but their different functions in carcinogenesis are largely unknown. We used real time quantitative RT-PCR to analyse survivin variants' mRNA expression levels in 77 gastric carcinoma cases whose frozen samples were available. All the cases and seven cell lines tested expressed wild-type survivin mRNA, which was not only the dominant transcript, but also was a poor prognostic biomarker (P = 0.003). Non-antiapoptosis survivin-2B mRNA was negatively correlated with tumor stage (P = 0.001) histological type (P = 0.007) and depth of tumor invasion (P = 0.031) while survivin-DeltaEx3 mRNA showed a significant reverse association with apoptosis ( P = 0.019). These data demonstrated that survivin mRNA expression levels are of important prognostic value, suggesting the significant participation of survivin-2B and survivin-DeltaEx3 in gastric cancer development.