It may be essential to know the behavior and gene expression of osteoblasts cultured on chemically modified surfaces to understand their surface properties in vivo. The purpose of this study was to compare the initial cDNA cellular response to calcium (Ca)- and magnesium (Mg)-ion implanted titanium surfaces. Mg ions and Ca ions were implanted onto ground titanium using the plasma source ion implantation technique. The structural and surface properties of the specimens were analyzed by scanning electron microscopy, auger electron spectroscopy, and Rutherford back-scattering spectroscopy. The MTT assay was used for examining the attachment of MC3T3-El cells, and cDNA microarray was used for the identification of differentially expressed genes. After ion implantation, the surface roughness and morphology did not change. The atomic concentrations of Mg and Ca were similar, while the Ca ions had higher oxygen affinity than Mg ions. The MTT assay showed an increase in the cell attachment on the Mg- and Ca-implanted surface. In the cDNA microarray analysis, the Ca-implanted surface showed more upregulated gene expression than the Mg-implanted surface. Also, the biocompatibility-related genes were expressed more on the Ca-implanted surface.