Foetal development and growth can be influenced by environmental factors. We have previously demonstrated that the smallest porcine foetus within a litter develops a higher proportion of fat and connective tissue in its muscles than the largest littermate. The present study aims to highlight the molecular mechanisms involved in this variation. Twenty-three pairs of porcine foetuses ranging from 36 to 86 days of gestation were used. The transcription rate of eight genes involved in cell growth and lipid synthesis was measured in the m. semitendinosus of the smallest and largest littermates together with the immunocytochemical localisation of myosin and IGFBP-5. Results showed that the myosin-expressing area was reduced in the smallest littermate supporting an increased proportion of connective tissue growth at the expense of muscle. IGF-1, IGF-1R, IGFBP-5, PPARgamma and myostatin mRNAs were upregulated in the smallest littermate, while IGF-2 was down-regulated and MyoD as well as CTGF were unaffected. The IGF system controls the growth of many cell types including cells of the extracellular matrix and skeletal muscle, but IGFBP-5 protein was predominantly localised in the extracellular matrix with a denser staining in the smallest littermate. In light of this, we propose that IGFBP-5 may play a role in directing an increased IGF-1-stimulated connective tissue growth in the smallest littermate. PPARgamma promotes lipid deposition in both adipocytes and muscle fibres and increased expression in the smallest littermate concurs with our previous findings of increased fat content in this group. Similarly, the upregulation of myostatin, a negative regulator of muscle growth, in the smallest littermate suggests that this factor may be involved in regulating the reduced myosin-expressing area observed. In conclusion, IGFBP-5, PPAR-gamma and myostatin may play a role in regulating the compartmentalisation of muscle versus connective tissue in the intralitter variation model of prenatal nutrition.