We have isolated cDNA clones encoding acetylcholinesterase from mouse muscle and brain. The polymerase chain reaction was used to amplify cDNA clones from C2 myotubes encoding the entire open reading frame and large segments of the 5' and 3' untranslated regions. The muscle cDNA clones were used to isolate clones from a brain library encoding the same mRNA species. The mouse clones encode a catalytic subunit containing a C-terminal sequence similar to that of the hydrophilic species of Torpedo. The mouse acetylcholinesterase sequence shares approximately 88% and 61% amino acid identity with bovine and Torpedo acetylcholinesterases, respectively, but only 52% identity with mouse butyrylcholinesterase, the sequence of which we have also deduced by molecular cloning. Northern blot and RNAase protection analyses indicate that the cDNA clones were derived from the acetylcholinesterase transcript that predominates in most expressing tissues. In contrast, erythroid cells are enriched in an mRNA species whose sequence diverges from that of the cDNA in the region encoding the C-terminus of the enzyme.