This study has demonstrated that it is crucial to determine the stability of reference genes under the specific experimental conditions employed. This is perhaps of paramount importance when studying the responses of cell types, such as macrophages, which are highly responsive to even subtle changes in the inflammatory milieu of their environment. We suggest a potential approach for the identification of stable reference genes for studying new experimental conditions. Initially, a review of the literature should be undertaken to identify several reference gene candidates. Next, if published array data is available, this can be used to identify genes whose expression levels remain unchanged under experimental conditions. Next, the stability of several candidate reference genes should be determined under experimental conditions by RT-qPCR. Finally, two or more programs should be used to identify the most stable reference gene. However helpful these programs may be in identifying the most stably expressed gene, it is still important to confirm the stability of the chosen genes by examining Ct values. For example, we have shown that, at 24 h, GeNorm identified a combination of genes as most stable, that were in fact regulated by LPS exposure, presumably because the algorithm used by GeNorm to rank stability assumes there is not co-regulation of the candidate reference genes.