Polycystic ovarian syndrome is a hormonal disorder which is very usual in women of reproductive age. The etiology of this disorder is due to environmental and genetic factors. The genetic factors which cause PCOS are mutations in Nuclear DNA, mt-mRNAs and mt-tRNAs. The highly conserved sequences of mt-tRNA genes are more vulnerable to such mutations. Current research was conducted to evaluate the mtDNA encoded tRNA^Cys gene in women suffering from PCOS. The information about patient’s weight, age, on set of disease etc was also recorded after getting informed consent. From 40 patients of District Abbottabad, about 10ml of saliva was collected in sterilized cups. The genomic DNA was extracted from collected saliva samples using phenol chloroform method. The PCR amplification of mt-tRNA^Cysgene was carried out and among them, 11 samples were redirected to TSINGKE Biological Technology (Cheng Du, China) for sequencing. The sequence results were compared with revised Cambridge Reference Sequence (rCRS) Accession Number (NC_012920.1) available at NCBI gene bank. No mutation was detected in either of the sequenced samples. It could be concluded that PCOS in subjects studied might not be due to mtDNA encoded tRNA^Cys gene mutation. However, it is therefore recommended that whole mitogenome should be sequenced in large sample set to evaluate the association of mtDNA mutations with PCOS.