A review of the literature identified eight candidate reference genes that have been used for the normalisation of gene expression data for BMDMs. We set out to evaluate the stability of these genes, and to identify any additional reliable reference genes. Microarray analyses of LPS stimulated BMDMs at 6 h and 24 h identified three candidate reference genes, whose expression remained unchanged between control and LPS treated cells. Two of the reference genes identified from the microarray analysis, Hnrnpab and Stx5a, were ranked as the most stable reference genes for normalisation of gene expression data, at both 6 h and 24 h. It should be noted that several commonly used reference genes, although not ranked in first or second position, were ranked in the top five for stability, and would, therefore, still be considered suitable for the normalisation of gene expression data. For example, at 6 h, Rpl13a, Hprt and Gapdh ranked third, fourth and fifth, respectively, according to NormFinder analysis. At 24 h, Actinb and Ppia were ranked third and fifth, respectively. Importantly, the current study identified several genes that should be excluded as reference genes under these particular experimental conditions, including Hmbs and Gusb after 6 h of BMDM exposure to LPS, and Gusb and B2m after 24 h LPS exposure. These genes were ranked lowest for stability by all three programs, and, therefore, their expression levels were clearly regulated by LPS exposure. The current study also indicates that B2m and Actinb are unsuitable candidates for normalisation of expression data at 6 h post-LPS stimulation, as their expression levels are modulated by LPS exposure, and, accordingly, these genes were ranked in the lowest five for stability by all three programs.