The mitochondrial enzyme, manganese superoxide dismutase (MnSOD) is an integral component of the cell's defense against superoxide-mediated cellular damage. We have isolated and characterized four cDNA clones and the structural gene for rat MnSOD. Northern analyses using MnSOD cDNA probes detected at least five mRNAs in all tissues and cell types examined. Southern and Northern analysis using a 3' non-coding sequence probe, common to all the cDNAs, showed hybridization only to genomic restriction fragments that correspond to our genomic clone and the five MnSOD mRNAs. These data demonstrate that all of the rat MnSOD transcripts are derived from a single functional gene. Primer extension data indicate that transcription initiation is clustered within a few bases. Northern analysis using intron probes demonstrates that all five transcripts are fully processed. Northern analysis using cDNA and genomic probes from sequences progressively 3' to the end of the coding sequence indicates that size heterogeneity in the MnSOD transcripts results from variations in the length of the 3' non-coding sequence. From this data and the location of potential polyadenylation signals near the expected sites of transcript termination, we conclude that the existence of multiple MnSOD mRNA species originate as the result of alternate polyadenylation.