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Abstract Alternative exon usage is known to affect a large portion of genes in mammalian genomes. Importantly, different splice isoforms sometimes possess distinctly different protein functions. Here, we analyzed data from the Human Epigenome Atlas for 11 different human adult tissues and for 8 cultured cells that mimic early developmental stages. We found a significant enrichment of cases where differential usage of exons in various developmental stages of human cells and tissues is associated with differential epigenetic modifications in the flanking regions of individual exons. Many of the genes that were differentially regulated at the exon level and showed deregulated histone marks at the respective exon flanks are functionally associated with development and metabolism.