This study aimed to assess the prevalence of seven periodontal marker pathogens, before implant placement and 1 yr after loading, in periodontally healthy individuals and to assess the long-term effectiveness of pre-implant reduction of pathogens to below threshold levels. In 93 individuals needing single tooth replacement, pooled subgingival microbiological samples from standard sites were cultured and analyzed before implant treatment and 1 yr after loading. Threshold levels commonly used in periodontology to predict periodontal breakdown were applied. Subjects with levels of pathogens above these thresholds received initial periodontal treatment including systemic antibiotics when indicated. At baseline, 49.5% of periodontally healthy subjects harboured one or more marker pathogens above threshold levels. Periodontal treatment reduced the pathogen levels below threshold values in 78.3% of these initially colonized subjects. In all cases Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis were reduced to below threshold. At 1 yr after loading, periodontal pathogens were present above threshold levels in 74.1% of all subjects. It is concluded that in almost half of periodontal healthy individuals the subgingival biofilm harbours periodontal pathogens above threshold values. Long-term effectiveness of pre-implant reduction of the selected marker pathogens appeared limited in our patient population, making pre-implant reduction unpredictive for post-implant levels of these pathogens. Thus, considering the applied microbiological criteria, generalized pre-implant microbiological testing is not contributory in periodontally healthy subjects.