Two alpha-amylase mRNAs which differ in the length of their 3' non-translated region accumulate in the cytoplasm in both mouse liver and salivary gland tissues. The two species in each tissue are transcribed from the same gene (Amy-1A). The minor species is approximately 20-nucleotides preceding the poly(A) tract. Sequence analysis of genomic DNA shows that these extra 237 nucleotides are specified by sequences contiguous to those shared by the two mRNAs. These data demonstrate that transcription can proceed through the major polyadenylation site and that alternative polyadenylation sites are used in the Amy-1A gene. Sequences which trail the two polyadenylation sites exhibit extensive homology and might therefore be involved in polyadenylation or transcription termination.