Marginal bone level is a criterion for implant success. The aetiological factors of bone loss have not been clarified. The aim of this study was to evaluate the influence of implant systems and prosthetic materials on the marginal bone loss. Twenty-three patients participated; two implant systems and three superstructure materials were used in this study. Twenty-two of the implants were restored with porcelain fused to base metal alloy (BMA), 25 with porcelain fused to noble metal alloy (NMA) and 20 with zirconium oxide-based ceramics. Radiographs were taken at baseline and 3, 6 and 12months after loading. Crestal bone-level changes were assessed with digital subtraction radiographs. The effects of superstructure materials and implants were evaluated with one-way anova and independent samples t-test, respectively (=0 center dot 05). The mean crestal bone loss was found 0 center dot 483mm in 3months, 0 center dot 622mm in 6months and 0 center dot 816mm in 12months. Prosthetic materials were found to have greater effect (=0 center dot 575, P=0 center dot 015) on crestal bone loss than implant systems (0 center dot 05). The porcelain fused to BMA restorations showed higher crestal bone loss than NMA-based restorations (P=0 center dot 003) at 3months, (P=0 center dot 038), at 6months and (P=0 center dot 00) at 12months; however, crestal bone loss differences between NMA and zirconia were not significant (P=0 center dot 629) at 3months, (P=0 center dot 974) at 6months and (P=1) at 12months. Within the limitations of this study, our results revealed that rather than the implant systems, prosthetic materials seemed to have an effective role on crestal bone.