The purpose of the present study was to compare the determination of the attachment level by probing and by measuring bone heights prior to and after the completion of a hygienic phase of periodontal therapy. 68 patients with moderate to severely advanced periodontitis underwent initial (hygiene phase) therapy including scaling and root planing, oral hygiene instructions and the elimination of plaque retention factors. Measurements of pocket probing depths, probing attachment levels and the location of gingival margins in relation to the cemento-enamel junction were performed at 4 aspects of each tooth with a thin calibrated probe at a baseline examination and 3 to 5 months following treatment. During these 3 to 5 months, the patients were kept in a maintenance care program. On the full-mouth radiographs obtained at baseline, the distance from the cement-to-enamel junction to the marginal alveolar crest was measured in millimeters and as a % of the root length. Furthermore, a subgroup of 11 patients, who were scheduled for modified Widman flap procedures, received another full-mouth radiographic examination before the surgical treatment. In addition, the level of the alveolar crest was assessed with a periodontal probe during the surgical procedure. The comparison of the different clinical and radiographic parameters showed the best correlations between the various radiographic measurements of bone heights (r = 0.87; r = 0.86). Clinical measurements of probing attachment level and probing level of the alveolar crest revealed slightly weaker correlations (r = 0.72). When comparing radiographic bone heights with clinical measurements of probing attachment levels, the lowest correlations were found (r = 0.65; r = 0.61; r = 0.61).