We have isolated a human genomic DNA cosmid clone while screening for the cathepsin L gene that, when sequenced, revealed close similarity with but significant differences from cDNA sequences that have been reported for cathepsin L (CTSL). The clone bears a novel sequence that shows 88% identity to the coding regions of the cathepsin L gene and a similar exon arrangement. We have called this sequence the "human cathepsin L-like gene 1" (CTSLL1). Translating putative exon sequences reveals a single premature stop codon; therefore no functional products are likely to arise from this gene. Fluorescence in situ hybridization (FISH) studies mapped the clone to chromosome 10q. Somatic cell hybrid mapping confirmed the location of CTSLL1 to human chromosome 10 distinct from the cathepsin L locus (CTSL) on chromosome 9. Furthermore, the FISH mapping studies show that a family of at least three related sequences exists on chromosome 10q, similar to the pattern of duplicated glutamate dehydrogenase (GLUD) gene loci reported on 10q. Using PCR and sequencing with genomic DNA samples, we have identified two additional novel related sequences (CTSLL2 and CTSLL3), and by PCR analysis of cDNA samples we have identified corresponding transcripts. Comparison of changes between our CTSLL1 sequence and the cathepsin L gene at mutation insensitive sites suggests that the two sequences arose from a duplication event 40-50 million years ago, and therefore at the time of divergence of early primates.