Epigenome-wide association studies (EWAS) investigate epigenetic modifications across the genome in relation to phenotypes of interest. The most commonly studied epigenetic modification in EWAS is DNA methylation, particularly at cytosine-phosphate-guanine (CpG) sites. Despite its potential, few EWAS have been conducted in bone diseases, and replication studies remain limited. Similar to genome-wide association studies, EWAS require rigorous steps for quality control of both samples and probes to ensure reliable results. Association analyses can focus on individual differentially methylated probes or adopt a regional approach to identify differentially methylated regions, providing insights into epigenetic contributions to disease.