12 patients were studied longitudinally to monitor the effects of basic periodontal therapy in molar and non-molar teeth. Periodontal sites were grouped into molar furcation sites, molar flat-surface sites and non-molar sites. Clinical measurements were taken at baseline and directly followed by full mouth root debridement. Subsequently, measurements were taken every 3rd month until 24 months. At each of these appointments, the patients were monitored for their oral hygiene performance and given supragingival prophylaxis. The mean results indicated that initially moderately deep and deep molar furcation sites responded less favorably to therapy compared to non-molar sites and molar flat-surface sites of similar probing depth. Initial improvements in probing measurements for moderately deep and deep molar furcation sites were limited and also tended to revert during the observation interval. Identification of individual sites with probing attachment loss disclosed that 25% of molar furcation sites lost probing attachment as compared to 7% for non-molar sites and 10% for molar flat-surface sites. These results corroborate previous findings and call for additional or alternative treatment regimens for periodontal furcation pockets.