The aims of this study were to compare clinical and microbiological features in the peri-implant area of implants carrying either screw retained or cemented suprastructures, and to investigate the relationship between the peri-implant microflora, the microbiota on the inner surface of removable suprastructures, and the periodontal microflora within the same subject. In 15 partially edentulous patients with ITI implants used as abutments for crown and bridge reconstructions, microbial samples were taken i) from the deepest periodontal pocket of each quadrant, ii) from the sulcus of the implants and iii) from the internal surface of the screw retained suprastructures. The samples were cultured using continuous anaerobic techniques. Five patients were found with both screw retained (S) and cemented (C) suprastructures. In these subjects the mean total cultivable counts were significantly higher in peri-implant samples from group C than in samples from group S. Furthermore, peri-implant samples of group S yielded a higher proportion of coccoid cells in the darkfield microscope and demonstrated absence of large spirochetes. From the 15 patients, Porphyromas gingivalis was detected in 10% of the periodontal samples and in only one peri-implant sample. Prevotella intermedia was detected in 33% of the periodontal and in 30% of the peri-implant samples. Fusobacterium spp. had a prevalence of 58% in the periodontal samples and was recovered from 50% of the peri-implant samples. Actinobacillus actinomycetemcomitans was not detected in any dental or peri-implant sample. In 1 case, however, the organism was recovered from the internal surface of the suprastructure. Linear regression analysis showed a significant relationship between the frequency of micro-organisms in peri-implant samples of group S and in samples from the inner surface of the suprastructure. Furthermore, there was a significant correlation between the incidence of micro-organisms in dental samples and i) in peri-implant samples of group S and ii) in samples from the internal suprastructure surface. These findings indicate, that the microbial leakage through the gap between the suprastructure and the abutment plays an important role in the bacterial colonization of the internal part of screw retained crowns and bridges. The study furthermore confirms the impact of the dental microflora on the microbial colonization of implants. This factor appears to be more important than the mode of fixation of the suprastructure.