Choline acetyltransferase (ChAT) and the vesicular acetylcholine transporter (VAChT) are both encoded by the cholinergic gene locus from which, in the rat, five different species of ChAT mRNA and three different species of VAChT mRNA are produced. So far, discrimination between mRNA subtypes has been possible only in CNS homogenates or in cell cultures. In this study, cardiac neurons were microdissected from frozen sections of rat heart using a u.v. laser and harvested using a micromanipulator. RT-PCR demonstrated the expression of the non-coding R-exon and splicing to R1-type mRNA in the majority of cardiac neurons. The technique presented here is the first to allow subtype analysis of cholinergic locus mRNA species in neurons in situ.