The purpose of this study was to compare histologic and morphometric procedures of bone height measurement. Microscopic measurements are the most frequent methods in periodontal studies with animals, but have limited capacity to identify bone levels associated with both healthy tissues and periodontal disease. Ligatures were placed in the maxillary left second molars of 10 male 60-day-old Wistar rats for 30 days. Left and right maxillary sides of 5 rats were processed for histologic analysis (H), sectioned buccolingually, and stained with HE. The maxillae of the other 5 rats were defleshed and used for morphometric analysis (M). Histometric measurements from the cementoenamel junction to the bone crest were performed. Standardized photographs were used for morphometric analysis. The t test was used for dependent or independent samples (alpha = 0.05%). Distances from cementoenamel junction to bone crest were 0.95 +/- 0.25 and 1.07 +/- 0.30 mm for H and M, respectively. Buccal measurements were 0.92 +/- 0.16 and 1.08 +/- 0.35 mm for H and M. The values obtained using H and M for areas without ligatures were 0.44 +/- 0.15 and 0.47 +/- 0.11 mm for lingual measurements and 0.23 +/- 0.08 and 0.41 +/- 0.10 mm for buccal measurements. No significant differences were found between the two methods in the detection of bone height associated with the placement of ligatures in rats.