The rat alpha 2,6-sialyltransferase gene produces three different sized mRNAs (4.7, 4.3, and 3.6 kilobases (kb)) which exhibit striking tissue-specific expression. Recently, we characterized the cDNA and genomic organization of the 4.3-kb mRNA which is unique to rat liver. In this report cDNAs of the 4.7-kb mRNA found in most tissues and the 3.6-kb mRNA(s) unique to kidney have been cloned and characterized as well as the corresponding genomic sequences which differed from those of the previously characterized 4.3-kb mRNA. The 4.7-kb mRNA was found to be identical to the 4.3-kb mRNA with the exception of two additional exons at the 5'-untranslated end of the transcript. The constitutively expressed 4.7-kb mRNA therefore codes for the same sialyltransferase as the liver-restricted 4.3-kb mRNA. The additional 5'-exons of the 4.7-kb mRNA are located at least 15-40 kb upstream of the promoter responsible for the production of the 4.3-kb liver message. The 3.6-kb mRNA of rat kidney was found to be comprised of three transcripts of similar size. They were only expressed in kidney and were found to be generated from the alpha 2,6-sialyltransferase gene by alternative splicing and alternative promoter utilization. The results reveal the complexity of the alpha 2,6-sialyltransferase gene which produces at least five transcripts via alternative splicing in a tissue-specific fashion.