Purpose: The aim of this study was to compare, in vitro, external-hexagon and Morse taper implant systems with respect to bacterial sealing between implants and abutments using a new methodology. Materials and Methods: Two groups of implants were tested. Group 1 implants had an external-hexagon implant-abutment interface (Neodent) and group 2 implants featured a Morse taper (Neodent) interface. The implants were perforated apically with a 1-mm bur until the bur reached the internal chamber. Prosthetic components were adapted with the recommended torque (32 and 10 Ncm, respectively) for each group. The implants were attached to an assay vial, with the abutment end positioned into the tube. With a sterilized syringe, the assay vials were filled with liquid culture medium (brain heart infusion broth). All the specimens were sterilized by gamma radiation. After the efficacy of sterilization had been confirmed using control samples, the apical hole was carefully opened and inoculated with Escherichia coli. Results: Samples were examined daily for evidence of contamination. Within a 14-day period, 60% of the samples of group 1 were contaminated and 30% of group 2 samples were contaminated. After this period there was no further contamination in either group. Conclusion: Although both systems exhibited bacterial contamination, the Morse taper implants of the system used in this study provided a better bacterial seal than external-hexagon implants of the same system. Keywords: contamination, dental implants, microbiology