Aggrecan is the major component of intervertebral disk matrix proteoglycan with multiple functional domains. To understand the role of aggrecan polymorphism in a part of exon 12 encoding the CS1 domain in lumbar disk degeneration disease, we have analyzed genomic DNA from 71 patients with the disease and 108 healthy individuals in northern Iran. The AGC1 alleles were determined by PCR followed by gel electrophoresis. Twelve AGC1 alleles ranging from 18 to 29 repeats were detected in patients and controls. The most frequent AGC1 allele was 27, followed by 28 in patients and controls. The shorter AGC1 alleles (< or =24 repeats) were more frequent in patients than in controls (37 vs. 16%, P < 0.001). The odds ratio for lumbar disk degeneration was 3.28 (95% confidence interval 1.62-6.65) in carriers of the shorter AGC1 alleles. Our data suggest that carrying shorter AGC1 alleles with less than 24 repeats could predispose a subject to lumbar disk degeneration disease in northern Iran.