The objective of the present study was a morphometric and morphologic analysis of maxillary and mandibular first and second molars using three different techniques. Measurements of 207 maxillary molars (105 first and 102 second molars) and 207 mandibular molars (110 first and 97 second molars) were measured; root length, radicular trunk length (RTL), mesiodistal and buccolingual diameters (BLD) at the cementoenamel junction, inter-radicular angle (IRA) width, and furcal roof area (FRA) were recorded. No significant statistical correlations were found for most of these measurements, the only exception being the relationship between IRA/FRA, IRA/BLD in maxillary molars, and IRA/RTL in the maxillary first molar. Morphologic examination was carried out by stereo microscopy, light microscopy of undecalcified sections, and scanning electron microscopy. All of thse techniques showed the complexity of the furcation area with a large number of anatomic irregularities and plaque-retentive structures that could hamper adequate cleaning during peridoontal treatment.