OBJECTIVES The aim of the study was to investigate the clearance of PVP-iodine applied as a gel or solution in periodontal pockets. METHODS Teeth of 12 subjects with at least eight periodontal pockets of ≥5 mm probing depth were isolated with a rubber dam to allow contamination-free access to the pockets. In each subject, three pockets were filled with PVP-iodine gel (10%) and three with PVP-iodine solution (10%). One pocket of each subject without iodine application served as a negative control. The treatment allocation was assigned randomly. Any excess material was removed subsequently. After 1, 5 and 15 min, a paper point was used to collect the sulcus liquid and the concentration of PVP-iodine was chemically determined. In addition, PVP-iodine gel was administered into 12 periodontal pockets immediately after sub-gingival ultrasound debridement and the concentration of PVP-iodine was determined after 1 min. RESULTS Descending concentrations of PVP-iodine were determined at 1, 5 and 15 min after the application. No PVP-iodine was found in the pockets serving as negative controls. The mean concentrations of the gel and solution were 6.14 μg/ml and 4.44 μg/ml (1 min; p ≥ 0.028), 3.20 μg/ml and 1.44 μg/ml (5 min; p ≥ 0.126), 0.69 μg/ml and 0.23 μg/ml (15 min; p ≤ 0.019), respectively. In the pockets with previous debridement the mean concentration was 1.68 ± 1.97 μg/ml. CONCLUSION The application of PVP-iodine gel in periodontal pockets allows a prolonged remnant effect as compared to that of the solution formula.