The callipyge mutation in sheep results in post-natal skeletal muscle hypertrophy in the pelvic limbs and loins with little or no effect on anterior skeletal muscles. Associated with the phenotype are changes in the expression of a number of imprinted genes flanking the site of the mutation, which lies in an intergenic region at the telomeric end of ovine chromosome 18. The manner in which these local changes in gene expression are translated into muscle hypertrophy is not known. Microarray-based transcriptional profiling was used to identify differentially expressed genes in longissimus dorsi skeletal muscle samples taken at birth and 12 weeks of age from callipyge and wild type sheep. The phenotype was only expressed at the latter developmental time and associated with decreased Type 1 fibres (slow oxidative) and a shift toward Type IIx and IIb fibres (fast-twitch glycolytic). We have identified 131 genes in the samples taken at 12 weeks of age that were differentially expressed as a function of genotype but which were not due to the fibre type changes. The gene expression changes occurring as a function of genotype in the samples taken at birth indicated that the transcriptional framework underpinning the phenotype was emerging prior to expression of the phenotype. Eight genes were differentially expressed as a function of genotype at both developmental times. A model is proposed describing a core network of genes and histone epigenetic modifications that is likely to underpin the fibre type changes and muscle hypertrophy characteristic of callipyge sheep.