We report the genomic organization of the mouse and rat genes coding for the 2460-amino-acid microtubule-associated protein (MAP) 1B. In addition to seven exons that encode full-length MAP1B, we have identified two alternative exons, exon 3A and the novel exon 3U. We demonstrate that alternative MAP1B transcripts containing either exon 3A or exon 3U are expressed in a variety of mouse and rat tissues at about 1 to 10% of the level of regular transcripts. The alternative transcripts, if translated, would give rise to MAP1B isoforms truncated at the N-terminus. The exon/intron organization underlying the alternative transcripts and the N-terminal amino acid sequence of the putative truncated MAP1B isoforms resemble those of MAP1A, providing further evidence for an evolutionary relationship. The detection of alternative transcripts has implications for the interpretation of conflicting results recently obtained in MAP1B knockout mice.