Intramuscular fat percentage (IMF%) is an important trait to the beef industry, but the mechanisms that underpin the variation are not entirely clear. We have analysed genome-wide mRNA expression profiles in LM muscle biopsies from two separate cattle experiments. Firstly, samples from a time course of the development of Wagyu x Hereford (high marbling) and Piedmontese x Hereford (low marbling) animals (3 each cross) on the same diet were profiled. A set of genes whose expression appeared most likely to be related to the differences in marbling was identified. The genes included CIDEA, ADIG, S100G, PCK1, PLIN1, FABP4, ADIPOQ, PSL1, AGPAT2, DGAT2, CIDEC and TUSC5, many of which are involved in the synthesis and storage of triacylglycerides (TAG). Secondly, samples from 48 Brahman steers were profiled and IMF% was measured at slaughter. We investigated the correlation between each of the genes on the array and the IMF% across the 48 animals. The genes identified in the first analysis were highly enriched amongst the genes whose expression levels were most positively correlated with IMF%.. Interestingly, when the 48 animals were separated on the basis of their Hormone Growth Promotant (HGP) treatment correlation of these genes with IMF% was increased in the HGP-treated animals and was not significant in the untreated animals. Overall the results support the hypothesis that increased IMF% is primarily associated with the increased ability of intramuscular adipocytes to store TAG, as opposed to increased synthesis or decreased degradation of lipids, which may occur in organs elsewhere.