Objectives: Alveolar bone crest level is essential in determining the need for bone removal in subjects with altered passive eruption (APE). This study assessed the validity of Cone Beam Computed Tomography (CBCT) and transgingival probing. Methods: Patients presenting with APE were assessed. Transgingival probing was performed to clinically assess the distance between the cementoenamel junction (CEJ) and the crest of the bone at the mid-point of upper anterior teeth. CBCT was used to assess this distance at the same point. Upon reflection of a full mucoperiosteal flap the actual distance was measured. Results: Similar actual and CBCT measurements of the distance between the CEJ and bone crest at upper right 3, upper left 2 and upper left 3 (P>0.05) were recorded. However, in upper right 2, upper right 1 and upper left 1 the distance was significantly greater on CBCT (P<0.05). No significant difference was detected between transgingival probing and the actual distance at all teeth assessed. Conclusions: Careful transgingival probing provides an accurate measure of the distance between the CEJ and crest of the Bone. CBCT gives an accurate estimate, However, it might not be justified for each patient in the presence of safer methods.