Recently, Na+/Pi cotransport activity has been demonstrated in rat liver hepatocytes. Here, we report the isolation of two Na+/Pi cotransporter cDNAs (RNaPi-1a and RNaPi-1b) from a rat liver cDNA library. The two cDNAs have the same coding but different 5'-untranslated regions. The rat cDNAs encode a polypeptide of 465 amino acids, having 62% and 66% identity with the rabbit NaPi-1 and human kidney Na+/Pi cotransporter, respectively. Northern blot analysis showed that a RNaPi-1a--specific probe detected two major transcripts (2.3 and 1.8 kb), whereas a RNaPi-1b--specific probe hybridized with one transcript (1.8 kb) in rat kidney, liver, and hepatocytes in primary culture. Rat liver expressed much higher levels of RNaPi-1a than RNaPi-1b, whereas the converse was true for rat kidney. Low levels of RNaPi-1 mRNAs were also detected in rat heart, brain, and skeletal muscle. These findings indicate that there are at least two isoforms of RNaPi-1 transcripts expressed in liver and kidney and that the levels of expression of the RNaPi-1a and RNaPi-1b may be controlled by tissue-specific factors.