The aim of this clinical study was to evaluate bacterial colonization, marginal bone loss, and optical alveolar density in implants with Morse taper (MT) and external hexagon (EH) connections. Thirty-five implants were installed in 7 patients (mean age: 65.8 ± 6.7 years). Implants were divided into 2 groups, according to platform design: G1 - MT, installed 2mm infra-osseous and G2 - EH, positioned according to Branemark protocol. Patients were evaluated at baseline (T0), 21 days (T1), 3 months (T2), 6 months (T3), and 12 months (T4) after installations. Bone loss and alveolar density were evaluated by standardized periapical radiographs and bacterial profile with checkerboard DNA-DNA hybridization. Statistical analyses were performed using SPSS 23.0. To present the results, boxplots and a line graph of mean were used. P-values ≤ .05 were statistically significant. After 3 months, alveolar bone loss was significantly higher in the G2 (T2-T0: P = .006; T3-T0: P = .003; and T4-T0: P = .005). No significant differences between G1 and G2 groups were observed for optical alveolar density. Microbiological analysis showed similar profiles between studied groups; however, there were significantly higher counts of Tannerella forsythia (P = .048), Campylobacter showae (P = .038), and Actinomyces naeslundii (P = .027) in G1 after 12 months. Based on the results of this study, it can be concluded that there was less peri-implant bone loss in MT compared to EH connections, but microbiological profile did not seem to influence bone changes.