The Sda blood group carbohydrate structure, GalNAcbeta1-4[NeuAcalpha2-3]Galbeta1-4GlcNAc-R, is expressed on glycolipid and glycoprotein in human gastrointestinal mucosa. The expression of the Sda determinant dramatically decreases in cancer tissue. The activity of the beta1,4N-acetylgalactosaminyltransferase (Sda-GalNAcT), which transfers GalNAc to NeuAcalpha2-3Galbeta1-4Glc(NAc)-R, correlates with the expression of the Sda immuno-epitope. From the total RNA fraction of human gastric mucosa, we have amplified a cDNA segment by reverse-transcription-polymerase-chain reaction (RT-PCR), using primers designed according to the cDNA sequence of a murine beta1,4GalNAcT which synthesizes the Sda determinant. An RT-PCR product of 390 bp shared 85% nucleotide identity with the murine Sda-related beta1,4GalNAcT. This RT-PCR product hybridized to a transcript in mRNA prepared from human gastric mucosa. In RT-PCR using specific primers to this PCR product, Sda-GalNAcT mRNA was detected in all samples of normal stomach and small intestine examined and the majority of normal colonic specimens. Six out of nine cases of gastric cancer, and 9 out of 13 cases of colonic cancer failed to produce the target DNA. These results correlate with the beta1,4GalNAcT activity measured in the same samples. In conclusion, a segment of the cDNA for betal,4GalNAcT which determines expression of the Sda carbohydrate structure was obtained, and reduced transcription of this beta 1,4GalNAcT resulted in the disappearance of the Sda epitope in gastrointestinal cancer.