Background: Extracellular stimuli induce gene expression responses through intracellular signaling mediators. The p38 signaling pathway is a paradigm of the mitogen-activated protein kinase (MAPK) family that, although originally identified as stress-response mediator, contributes to establishing stem cell differentiation fates. p38 alpha is central for induction of the differentiation fate of the skeletal muscle stem cells (satellite cells) through not fully characterized mechanisms. Methods: To investigate the global gene transcription program regulated by p38 alpha during satellite cell differentiation (myogenesis), and to specifically address whether this regulation occurs through direct action of p38 alpha on gene promoters, we performed a combination of microarray gene expression and genome-wide binding analyses. For experimental robustness, two myogenic cellular systems with genetic and chemical loss of p38 alpha function were used: (1) satellite cells derived from mice with muscle-specific deletion of p38 alpha, and (2) the C2C12 murine myoblast cell line cultured in the absence or presence of the p38 alpha/beta inhibitor SB203580. Analyses were performed at cell proliferation and early differentiation stages. Results: We show that p38 alpha binds to a large set of active promoters during the transition of myoblasts from proliferation to differentiation stages. p38 alpha-bound promoters are enriched with binding motifs for several transcription factors, with Sp1, Tcf3/E47, Lef1, FoxO4, MyoD, and NFATc standing out in all experimental conditions. p38 alpha association with chromatin correlates very well with high levels of transcription, in agreement with its classical function as an activator of myogenic differentiation. Interestingly, p38 alpha also associates with genes repressed at the onset of differentiation, thus highlighting the relevance of p38-dependent chromatin regulation for transcriptional activation and repression during myogenesis. Conclusions: These results uncover p38 alpha association and function on chromatin at novel classes of target genes during skeletal muscle cell differentiation. This is consistent with this MAPK isoform being a transcriptional regulator.