Light chain 3 (LC3) is a subunit of the neuronal microtubule-associated proteins (MAPs), MAP1A and MAP1B. Recent findings show that the cDNAs for MAP1A and MAP1B encode polyproteins that contain the MAP1A or MAP1B heavy chain and a LC2 or LC1 subunit, respectively. We have sequenced a cDNA encoding rat LC3, and its sequence is not found in the MAP1A/LC2 or MAP1B/LC1 polyprotein cDNAs. The deduced amino acid sequence of LC3 is highly conserved between rat and mouse. Rat LC3 is a 16.4-kDa protein with a predicted pI of 9.2. It is encoded on a 1.7-kilobase mRNA. Our anti-LC3 antiserum shows that LC3 is abundant only in neurons and that the majority of LC3 in brain co-purifies with microtubules. Purified recombinant rat LC3 retains the ability to associate with microtubules assembled in the presence of brain MAPs and with microtubules assembled from purified tubulin. We propose that LC3 functions primarily as a MAP1A and MAP1B subunit and that its expression could regulate the microtubule binding activity of MAP1A and MAP1B.