Compounds, like beta-aminopropionitrile (bAPN) and homocysteine (hcys), are known to inhibit a stable matrix formation. Osteoblast-synthesized collagen matrix regulates the differentiation of precursor cells into mature osteoblasts. They express lysyl oxidase, an enzyme involved in the collagen cross-linking process. Lately, plasma hcys levels have recently been strongly correlated with fracture in humans. We have previously shown that bAPN not only disturbs collagen cross-links but also affects osteoblastic differentiation in a cell culture system. The aim of the present study was to investigate the effects of bAPN and hcys on collagen cross-links and gene expression at the mRNA level by FTIR and quantitative RT-PCR, respectively. We found that bAPN and hcys down-regulated cell multiplication. While bAPN also down-regulated the metabolic activity of MC3T3-E1 cells, hcys down-regulated it by lower concentrations but up-regulated it by higher; both substances up-regulated alkaline phosphatase activity. The substances increased the ratio of pyr/divalent cross-links of collagen, and down-regulated mRNA expression of lysyl hydroxylase (Plod2) and lysyl oxidase (Lox), genes which play an important role in the formation of a stable matrix. Furthermore, we demonstrate that both substances stimulated the expression of Runx2, an indispensable regulator of osteoblastic differentiation. However, analysis of genome wide mRNA expression suggests that hcys and bAPN have differential effects on genes involved in osteoblastic differentiation and phenotype regulation. The results indicate that although both bAPN and hcys affect collagen cross-link post-translational modifications in a similar manner as far as pyr and divalent cross-links are concerned, they have differential effects on the monitored genes expression at the mRNA level, with hcys exerting a broader effect on the genome wide mRNA expression.