Purposes: (1) To determine the effect of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and acidulated phosphate fluoride (APF) on S. mutans viability, (2) to observe their effects on biofilm structure, and (3) to examine the element content of the hydroxyapatite (HA) surfaces after exposure to CPP-ACP and APF. Methods: HA discs were coated with: CPP-ACP (GC Tooth-Mousse), APF, CPP-ACP+APF (1/1). Uncoated HA discs were used as control. Following application of the materials, the discs were immersed in human saliva and incubated with S. mutans ATCC (27315) for 24 hours. Growth of bacteria on the discs was evaluated by microbial culturing methods. The structure of the biofilm was examined with confocal laser scanning microscope (CLSM). The change in element content of HA surfaces (without biofilm) was evaluated with energy-dispersive x-ray spectroscopy (EDS). The values were statistically analyzed using Kruskal-Wallis and Dunn's test. Results: The total number of bacteria of APF and CPP-ACP+APF applied groups were found significantly lower than the control group (P< 0.05). All specimens showed similar microbial colonization structure. No statistically significant differences were observed in O, F, Na, P, Ca content on HA surfaces after exposure to the tested agents, although fluoride concentration of the APF treated HA surfaces were increased compared to CPP-ACP, CPP-ACP +APF. (Am J Dent 2011;24:119-123).