Full-length cDNAs coding for the human GM2-activator protein has been isolated and characterized, and its genomic structure studied in two overlapping clones in lambda-EMBL-4 isolated from a human brain genomic library. Two different cDNAs were found that were identical to the 5'-terminus to nt 1311 (counted from the A of the initiation codon, ATG) including the entire protein coding sequence. However, they were entirely dissimilar in the 3'-non-coding sequences. The genomic clones covered 94% of the full-length cDNA sequence. Three introns were found. The last exon spans contiguously the carboxyl terminus of the protein and the entire 3'-untranslated region of one of the two cDNAs with different 3'-ends. The origin of the 3'-portion of the other cDNA clone is not clear at this time.