Objectives: The microflora around and beneath restorations is an important factor of restoration failure. The aim of this pilot study was to determine and compare the microbial spectrum under composite and amalgam restorations with special attention to the anaerobic flora. Method and materials: Ten composite and five amalgam restorations scheduled for replacement were clinically evaluated for marginal gaps, fractures, and secondary caries. After their removal and caries diagnosis, a dentin sample just below the restoration was taken under sterile conditions, stored in a prereduced transport medium for anaerobic bacteria, and immediately transferred to a laboratory for microbial diagnosis. Results: The clinical parameters showing mostly moderate marginal imperfections and the ratios of aerobic to anaerobic flora were comparable for composite and amalgam restorations (11.4%:88.6% and 15.4%:84.5%, respectively). The microbial variety under composite restorations was much greater compared to amalgam, and it was similar to that of infected root canals including anaerobic gram-negative rods, such as Fusobacterium species or Porphyromonas species Beneath amalgam, the microbial flora was similar to the one found in carious dentin and plaque, with anaerobic and facultatively anaerobic gram-positive rods dominating. Quantitatively, there were up to eight times more microorganisms under composite restorations. The number of bacterial strains correlated with the caries activity and the filling material, the number of anaerobic rods correlated highly with caries activity and localization. In a linear regression, caries activity and the filling material had statistically significant influence on the bacterial load. Conclusion: Although caries activity and location had the greatest influence on the microbial flora under the restorations, the kind of restoration material seemed to have an additional effect on the composition of the microflora. This pilot study indicates that inadequate composite restorations may promote the growth of cariogenic, as well as obligate anaerobic and potentially pulpopathogenic bacteria, which should be confirmed by further studies.