Introduction: One of the criteria of implant therapy success is marginal bone loss. The objective of the study was to assess the correlation between peri-implant marginal bone loss and implant-abutment connection systems used in the same patient, as well as other specific characteristics of implant treatment. The initial research hypothesis assumed that there was no difference in marginal bone loss around implants with different implant-abutment connection systems placed in the same patient. Material and methods: Marginal bone loss was assessed around implants with two different types of implant-abutment connection: with conical (Type I) and with internal hexagonal (Type II) in the same patient. The study included 28 patients aged 37–66 years. The evaluation of marginal bone loss in the studied patient groups was made on the basis of orthopantomographic radiographs. Results: Marginal bone loss around Type I implants was 0.112 mm/month before loading with prosthetic restorations, and 0.010 mm/month after loading, while for Type II implants it reached, respectively 0.123 mm/month and 0.030 mm/month. Marginal bone loss after loading with prosthetic restorations was 11 times lower for Type I implants and 4 times lower for Type II implants. Conclusions: Implants with conical implant-abutment connection are significantly more favourable to osseointegration than those with internal hexagonal connection. As marginal bone loss is faster before loading implants with prosthetic restorations than after loading, it is advisable to consider early loading if the necessary clinical conditions are met.