The expression of predominant housekeeping genes used in RT-qPCR can vary during development and differentiation. The frequently used housekeeping genes (ACTB, GAPDH, 18S rRNA, EF1α and RPL 13a) were evaluated during an early stage of the osteogenic differentiation of mouse bone marrow-derived mesenchymal stem cells (mMSCs) (under normal conditions or treated with CCG-4986) to identify housekeeping genes whose expression remained constant during osteogenic differentiation. When we used RGS4 mRNA, which was determined as copy number per μg of total RNA, to normalize gene expression, we observed that the relative EF1α expression profile was consistent with RGS4 expression after treatment with CCG-4986. All the relative expression profiles of the EF1α, 18S rRNA, and RPL13a housekeeping genes were consistent with RGS4 profiles determined by measuring mRNA copies under normal osteogenic differentiation conditions. The expression profiles calibrated by ACTB and GAPDH were not consistent with those determined using mRNA copy number in untreated cells or cells treated with CCG-4986 under osteogenic differentiation conditions. Under normal osteogenic differentiation conditions, EF1α, 18S rRNA, and RPL 13a are suitable housekeeping genes for RT-qPCR analysis. However, EF1α is the only suitable gene upon CCG-4986 treatment.