The aim of the present study was to determine the molecular basis of the beneficial effects of genistein and/or menaquinone-4 (MK-4) on bone quality. Initially, 1 mu M genistein was applied to MC3T3-E1 cells for 24 h and the upregulated mRNAs that were detected by microarray were selected for further examination by reverse transcription-quantitative-polymerase chain reaction. Among them, alterations were observed in the level of GATA-binding protein 6 (GATA6), Notch gene homolog 2 (NOTCH2), Wnt family member 5A (WNT5A), bone.-carboxyglutamate protein (BGLAP), chondroadherin (CHAD), dipeptidyl peptidase 4 (DPP4), ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), alkaline phosphatase (ALP) 3 and ATPase phospholipid-transporting 11A (ATP11A) in response to treatment with 0.1 mu M 17-beta-estradiol, 1 mu M genistein, and/or 1 mu M MK-4. GATA6, NOTCH2 and WNT5A are considered to be associated with osteoclast, but not osteoblast, function; however, increases in osteoblastic mRNAs, including BGLAP and CHAD, were observed in each of the treatment groups at 48 h. Immunocytochemical analysis confirmed an increase in CHAD and DPP4 proteins following the administration of genistein + MK-4. Furthermore, genistein + MK-4 led to alterations in cell morphology to spindle or oval shapes, and increased the intensity of ALP staining. Although the level of ALP mRNA was not consistently altered in response to the treatments, a marked increase in ALP activity was observed following 96 h treatment with genistein + MK-4. Therefore, the simultaneous intake of genistein and MK-4 appears to be beneficial for the maintenance of bone quality.