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Poor nutrition during critical growth phases may alter the structural and physiologic development of vital organs thus “programming” the susceptibility to adult‐onset diseases and disease‐related health conditions. Epigenome‐wide association studies have been performed in birth‐weight discordant twin pairs to find evidence for such “programming” effects, but no significant results emerged. We further investigated this issue using a new computational approach: Instead of probing single genomic sites for significant alterations in epigenetic marks, we scan for differentially methylated genomic regions. Whole genome DNA methylation levels were measured in whole blood from 150 pairs of adult identical twins discordant for birth‐weight. Intrapair differential DNA methylation was associated with qualitative (large or small) and quantitative (percentage) birth‐weight discordance at each genomic site using regression …