This study analyzed the difference in effectiveness of a well-known manual toothbrush and a counterrotational electric toothbrush over medium- and long-term periods. Six dental students and six patients with moderate periodontitis participated in a split-mouth, single-blind experiment with repeated recordings of pocket depths and plaque and gingivitis indices. During the experiment, the use of interdental aids or mouth rinses was forbidden. At all intervals up to week 34, manual brushing resulted in significantly less plaque removal, especially at approximal sites. Use of the counterrotational electric toothbrush resulted in a significantly greater reduction in gingival inflammation and significantly increased pocket reduction, especially in the periodontitis group. A crossover experiment confirmed the inferiority of the manual cleaning. The long-term observations showed a slight decrease in efficiency of both brushes, thereby justifying the need for regular motivation reinforcement. The results of the current study demonstrate the long-term superiority of a counterrotational electric toothbrush over the manual toothbrush.