The structure of the gene for the human alpha 1(XIII) collagen chain (COL13A1) was determined from genomic clones spanning 140,000 base pairs (bp), including about 3,000 bp of the 5'-end-flanking region and 5,000 bp of the 3'-end-flanking region. The gene was shown to contain 39 exons. There were eight exons of 27 bp, five of 36 bp, four of 54 bp, three of 45 bp, and two of 42 bp. The rest of the exons coding for translated sequences had sizes varying between 24 and 153 bp. The genomic clones did not contain exons 3 and 4 whose sizes could, however, be estimated from cDNA clones. S1 nuclease mapping and primer extension analyzes indicated five closely spaced initiation sites of transcription. Sequencing of the 5'-end-flanking region did not reveal a typical TATA box but a four times repeated TATTTAT sequence that may serve as true TATA boxes. Two CCAAT boxes were found starting at positions-13 and -194, and furthermore, the promoter region contains two GC boxes. Previous studies on alpha 1 (XIII) collagen cDNA and genomic clones showed that the primary transcript undergoes complex alternative splicing generating at least four different forms of mRNAs. The present work demonstrated that sequences of seven exons are alternatively used. These exons contain sequences coding for pure collagenous regions, pure noncollagenous regions, and an exon coding for a junction of a collagenous and noncollagenous domain.