Fluorinated diamond-like carbon (F-DLC) coating is biologically safe, provides superior antibacterial properties, and shows promise in preventing postoperative peri-implant infections. However, potential negative effects of this coating on in vivo bone formation and resorption have not been studied. The authors investigated the effects of F-DLC coatings on bone union in beagle dogs. Seventy-two solid columns of titanium alloy were prepared with equally spaced slits. Half of these columns were coated with F-DLC (Group F), and the others were left uncoated as controls (Group C). Columns were implanted in the femurs of beagle dogs, and in vivo bone formation and resorption were assessed 4, 8, and 12 weeks after implantation. In comparison to Group C, Group F showed significantly greater bone volume and trabecular thickness at Week 8 (p < 0.05) and Week 12 (p < 0.005) and significantly lower bone resorption activity, measured by the ratio of osteoclasts to bone surface and of eroded surface to bone surface, at Week 12 (p < 0.05). The F-DLC coating encouraged bone formation in vivo more effectively than uncoated titanium alloy, suggesting that F-DLC will prove to be a useful coating material for antibacterial intraosseous implants.