Housekeeping genes like glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin are often used as internal standards for quantitative RNA analysis. In our study we analyzed the relative expression level of GAPDH and beta-actin as well as of the 18S rRNA and the Poly (A)+ RNA in growing collateral arteries in a rabbit model of arteriogenesis which is not associated with ischemia. Relative quantitation of the housekeeping genes displayed a significant upregulation of the beta-actin- and GAPDH mRNA during the first 24 h of vessel growth. For day 3 our results revealed an even stronger upregulation of the beta-actin mRNA (140%) but a significant downregulation of the GAPDH mRNA (50% of control). The 18S rRNA, however, showed for the same periods only minor alterations compared to the Poly (A)+ RNA. From these results we conclude that the 18S rRNA, but not the GAPDH- or beta-actin mRNA is an appropriate internal control for relative quantitation of gene expression under conditions of cell proliferation in growing vessels.