Nitric oxide (NO), generated from L-arginine by an enzymatic reaction of a NO synthase (NOS; EC 1.14.23), is a recently identified biological mediator suggested to be involved in a wide variety of biological processes. In the present work, we isolated and sequenced the entire region of cDNAs encoding mouse neuronal NOS (n-NOS) and demonstrated structural diversity of n-NOS mRNA in the nervous system. Sequence determination revealed a novel mRNA with an inframe deletion in the middle of the n-NOS cDNA. Structural analysis of the corresponding part of the n-NOS gene indicated that the deletion corresponded exactly to two exons. These findings suggest that the variant n-NOS is formed by alternative splicing. Both n-NOSs were found in almost all parts of the nervous system, the expression level of the novel variant being about one twentieth of that of the known n-NOS. Generation of diversity of n-NOS is probably related to diversity of its biological functions.