Objective To explore the relationships of variations in D-loop and COII-tRNA Lys intergenic region in mtDNA with PCOS. Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COII-tRNA Lys intergenic region in mtDNA were amplified and sequenced; sexual hormone assay, oral glucose tolerance test (OGTT) and insulin releasing test were carried out. Then variations found in mtDNA were compared between the two groups, the correlations between variations and clinical indexes were analyzed in all subjects. Results Nucleotide variations found in mtDNA were not different between the two groups, but the mutation of 16 094T/C was found associated with the serum levels of T and fasting insulin; (303-317)Cn TCn associated with the serum levels of A and LH; 195C/T with A level and 491T/C with LH level; (8 272-8 289)(ACCCCCTCT)n was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA perhaps associate with PCOS clinical symptoms and involve in PCOS development. Objective To explore the relationships of variations in D-loop and COII-tRNA Lys intergenic region in mtDNA with PCOS. Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COII-tRNA Lys intergenic region in Then the mutant found in mtDNA were compared between the two groups, the correlations between variations and clinical tests were analyzed in all subjects. Results Nucleotide variations found in mtDNA were different between the two groups, but the mutation of 16 094T / C was found associated with the serum levels of T and fasting insulin; (303-317) Cn TCn associated with the serum levels of A and LH; 195C / T with A level and 491T / C with LH level; (8 272-8 289) (ACCCCCTCT) n was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA may associate with PCOS clinical symptoms a nd involve in PCOS development.