To assess the effect of concomitant subgingival rinsing with 10% PVP-iodine during subgingival instrumentation on the prevalence and magnitude of bacteraemia of oral origin. Subgingival instrumentation was performed with water or PVP-iodine rinse in patients with periodontitis. Prior to instrumentation, subjects gargled for 1 min with the allocated liquid. Pockets were then rinsed for 1 min and subgingivally instrumented with liquid-cooled (water/PVP-iodine) ultrasonic scalers (1 min). Two minutes later, a blood sample from the arm vein was drawn using a lysis centrifugation blood culture system for quantitative microbiological analysis. Non-parametric statistical tests were performed to assess differences in the prevalence and extent of bacteraemia between groups. Of the 19 samples in each group, oral-borne bacteraemia was detected in 10 of the control and 2 of the test samples. With an average of 3.0 [1; 5] colony forming units, significantly less bacteria and bacteraemia were found in the test group compared to the controls (12.2 [1; 46]) (p = 0.003). Anaerobic bacteria were not found in the test group. Bacteraemia after subgingival instrumentation with concomitant PVP-iodine rinsing is reduced but not eliminated. Therefore, it might be recommended for patients at a high risk of endocarditis or infection of endoprostheses. However, preventive antibiotic treatment should not be omitted.