Purpose: To determine the three-dimensional (3D) tooth morphology of all primary molars and to identify and consolidate positional factors that could potentially have an effect on tooth preparation. Study design: Thirty-one non-carious primary molars were scanned using micro-CT and reconstructed using 3D analysis software. Each pulp horn to its respective cusp tip distance (PHCD) was measured as well as the distances from the pulp chamber to the mesial, distal, lingual and buccal surfaces. One-way ANOVA and post-hoc t-tests were used for data analysis. Results: The mesio-buccal and disto-buccal PHCD was significantly shorter than the mesio-lingual and disto-lingual PHCDs in maxillary second primary molars (P < 0.05). Mesial, distal and lingual walls were thinner than the buccal walls of mandibular molars while in maxillary molars; the mesial and distal walls were thinner than the palatal and buccal walls (P < 0.05). Conclusions: First primary molars have thinner tooth structure surrounding the pulp than second primary molars in the same arch with the exception of the buccal walls of all molars and lingual walls of maxillary molars. The mesial and distal walls are thinner than the buccal walls of all molars and lingual walls in maxillary molars.