Liver plays a central role in the regulation of the metabolic status, partitioning of nutrients and expenditure of energy. In order to gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition, liver expression profiles were compared of pigs of two breeds, the obese German Landrace (DL) and the lean Pietrain (Pi). Porcine oligonucleotide microarray were hybridised with liver cRNAs obtained at peri-pubertal age (180 days of age) and prenatal stages (35, 63, and 91 days post conceptionem) that represent three developmental stages of liver, i.e. period of differentiation, period of metabolic activity and period of glycogen accumulation. In terms of number of genes regulated between DL and Pi the most striking distinction were found at peri-pubertal age with upregulation of key genes of lipid metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs and upregulation of genes of cell growth and/or maintenance, protein syntheses as well as cell proliferation pathways (PPARD, POU1F1, IGF2R) in lean Pi pigs. Moreover, time course analysis of breed dependent expression profiles revealed breed-typical temporal regulation from prenatal stages to peri-pubertal age of genes assigned to biological processes involving lipid pathways and cell activity, i.e. breed differences are already initiated during early prenatal development. Information about mRNA expression levels of the two breeds differing in body composition, partitioning and utilisation of nutrients and energy reveals functional candidate genes for traits related to obesity and leanness.