The aim of this study was to measure subjective intensities of pain during the treatment of periodontal lesions with the Vector-system when compared to pain occurring during the treatment with conventional methods. Twenty patients, each of whom had three teeth with comparable periodontal pocket depths, were treated using three different methods: (i) scaling and root planing with hand instruments, (ii) cleaning with a conventional ultrasonic instrument (Siroson S) and (iii) cleaning with the Vector-system. The subjective intensities of pain during the treatment were measured with an intermodal intensity comparison. A visual analog scale was used for the evaluation after the treatment. The results of the intermodal intensity comparison during treatment showed that the use of the Vector-system caused less pain than the cleaning with hand instruments or the conventional ultrasonic system (P < 0.05). The intermodal intensity comparisons of cleaning with hand instruments and cleaning with the conventional ultrasonic system were not significantly different (P > 0.05). These results could be confirmed by the visual analog scale. Using the Vector-system for cleaning periodontal lesions it is possible to reduce pain sensations compared to conventional methods. Using cleaning methods that cause less discomfort and pain, it might be possible to increase the patient's compliance during non-surgical periodontal therapy and recall.