Background <p>Children with intellectual disability are more likely to experience chronic and neuropathic pain, which remains frequently under-recognized due to limitations in self-reporting and objective assessment tools. Epigenetic mechanisms, particularly DNA methylation, are believed to influence pain perception. This study investigates the differences in methylation patterns between children with intellectual disability and their age- and sex-matched neurotypical controls.</p> Methods <p>A cross-sectional study was carried out from March 2022 to July 2023 at the IRCCS Burlo Garofolo in Trieste, Italy. The methylation profiles of children with severe to profound intellectual disabilities and a history of recurrent pain episodes were compared to those of healthy controls. Whole blood DNA was analysed through bisulfite conversion and microarray technology, focusing on CpG islands, gene regions, and enhancers.</p> Results <p>Seventy-two participants were enrolled, including 36 children with intellectual disability and 36 without. The analysis identified four Differentially Methylated Regions (DMRs). DMR1, located within the *RNF39* gene, was found to be hypomethylated in children with intellectual disabilities. Similarly, DMR2, upstream of *VTRNA2-1* and *MIR886*, and DMR4, at the 5’UTR of *AURKC*, were also hypomethylated. In contrast, DMR3, positioned upstream of *IRF6*, was hypermethylated in the intellectual disability group.</p> Conclusions <p>These findings indicate that children with intellectual disability exhibit distinct methylation patterns of genes related to pain pathways compared to their healthy peers. Additional research is needed to investigate the clinical relevance of these epigenetic alterations and their potential as biomarkers for pain in this population.</p>