Polycystic ovary syndrome (PCOS) is often associated with aberrant DNA methylation. Despite the advances in diagnostics and treatment of PCOS, the pathophysiological mechanism remains unknown. Several genes are epigenetically dysregulated in PCOS and associated with pathological consequences of PCOS and metabolic comorbidities; however, the methylation status of specific genes and to what extent the genes are deregulated in terms of methylation pattern are unknown. This review aimed to analyse the existing data for specific genes and find conclusive evidence of their involvement in PCOS and associated risks. A comprehensive literature search was conducted in five electronic databases. The case-controlled clinical studies using both PCOS and healthy women and evaluating the methylation pattern without any treatment or intervention were included in the study. A random-effect model was used to extract the data for meta-analysis, and outcomes were expressed as standardized mean difference with a 95% CI. From 541 screened records, 41 studies were included in the review and 21 of them were used for meta-analysis of 20 genes. Meta-analysis revealed a significant global DNA hypomethylation in different tissues and peripheral blood of patients with PCOS compared to healthy controls. Specific gene methylation assessment revealed that genes associated with several functions were significantly hypomethylated and hypermethylated in patients with PCOS. This review provides conclusive evidence of epigenetic deregulation of specific genes in PCOS. These genes can potentially be used to develop diagnostic biomarkers or as targets for personalized therapy.