The current study identified the most stably expressed genes for use in the normalisation of gene expression data during the course of the pro-inflammatory response of primary murine macrophages to LPS. The two most stably expressed genes were identified from microarray analyses of BMDMs exposed to LPS, and, here, make their debut as reference genes. The data presented also confirms the stability of other reference genes used previously in the literature for normalisation of gene expression data in this inflammatory BMDM model. Importantly, we have identified several “traditional” reference genes that are often assumed to be stable, whose expression levels are, in fact, strongly regulated during the BMDM inflammatory response to LPS. We recommend that these genes not be used for the normalisation of gene expression data in this model, due to the likelihood of erroneous results, and the potential for invalid experimental conclusions to be drawn. This also highlights the need for experimental validation of reference gene stability under specific experimental conditions, and we have outlined a potential approach for identifying stable reference genes.