Peroxisome proliferator-activated receptors (PPARs) belong to a family of nuclear receptors. To date, three types of PPARs, namely PPAR alpha, PPAR delta, and PPAR gamma, have been identified, demonstrating co-expression across numerous tissues. PPAR gamma is primarily distributed in adipose tissue, the colon, the immune system, and the retina, while PPAR alpha is predominantly expressed in metabolic tissues such as brown adipose tissue, the liver, and the kidneys. Both PPAR gamma and PPAR alpha play crucial roles in various cellular processes. Recent data suggest that the PPAR family, among other mechanisms, might also be regulated by epigenetic mechanisms. Our recent studies, alongside numerous others, have highlighted the pivotal roles of DNA methylation and histone modifications in the regulation of PPAR gamma and PPAR alpha, implicating them in the deterioration of metabolic disorders via epigenetic mechanisms. This still not fully understood mechanism of regulation in the nuclear receptors family has been summarized and described in the present paper. The present review summarizes the available data on PPAR gamma and PPAR alpha regulation via epigenetic mechanisms, elucidating the link between the development of metabolic disorders and the dysregulation of PPAR gamma and PPAR alpha resulting from these mechanisms.