Fluoride is a reductive agent and may modify the oxide layer of titanium (Ti) in the transgingival region of dental implants. The low pH and the high fluoride concentration of prophylactic mouthwashes and gels (used in caries prevention) may play a role in this phenomenon. Our main goal was to examine whether changes on the surface structure of Ti caused by high fluoride concentration and acidic pH alter the adherence and the colonization of bacteria. Polished commercially pure Ti discs (CP grade 4, Camlog, Biotechnologies AG, Switzerland) were used in the study. Each sample was treated for 1 hour with one of the solutions: mouthwash containing 0.025% (250 ppm) fluoride, a gel containing 1.25% (12500 ppm) fluoride, and a solution of 1% NaF (3800 ppm fluoride), pH 4.5. The surface structure of the discs was analyzed by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). The colonization of Streptococcus mutans was studied by scanning electron microscope (SEM) after a 5-day incubation period. The roughness of the treated sample surfaces (Ra), as revealed by AFM measurements, increased 1.3 times for the gel and the mouthwash, and approximately seven folds for the 1% NaF solution, as compared to the control surface. The high fluoride concentration and acidic pH of the gel and the 1% NaF solution resulted in a strong corrosion and a modification of the composition of the Ti surface. The XPS spectra showed the formation of a fluoride containing complex (Na2TiF6) bound strongly to the surface. A correlation was revealed between the roughness of the surface and thickness and maturity of the S. mutans bacterial colonies developed on the modified Ti surface. High fluoride concentration and acidic pH increased the roughness of the Ti surface. Bacterial biofilm colonization on this rough surface proved to be more mature. The amount of bacteria was increased due to the changes in the surface caused by fluoride treatment. The present study indicates that high fluoride concentration in an acidic pH environment may affect the development of a healthy transgingival epithelial junction on the Ti surface. This work was supported by the SIMI-NAS Project of the 5th FWP of the European Commission (Growth Program, GRD3-2001-61801), the Hungarian Ministry of Economy and the EC (GVOP-3.2.1.-2004-04-0408/3.0), the Hungarian Ministry of Health (ETT, 434/2006), and the Hungarian Scientific Research Fund (OTKA F-68440).