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Abstract Objective To investigate the spatial changes of unopposed molars within the period between the antagonist extraction and the final implant restoration using data from cone beam computed tomography. Methods A total of 59 patients with 68 unopposed molars were included in this study. Three-dimensional models reconstructed from cone beam computed tomography data before and after loss of the antagonist were superimposed to measure the spatial changes. The overeruption and tipping of target teeth were calculated by coordinate values. Results The result of overeruption over the study period (9.2 ± 4.3 months) was expressed by two values: the mean overeruption of molar cups (0.432 mm) and the maximum overeruption of cusps (0.753 mm), which were statistically significant compared to the baseline level (p < 0.001). The average tipping was 1.717 degrees in the buccal direction. Conclusions Unopposed molars displayed overeruption throughout the study period (9.2 ± 4.3 months), which indicates that the clinicians should pay attention to the possibilities of overeruption and make appropriate interventions in their clinical practice. The establishment of three-dimensional measuring methods using cone beam computed tomography data helps analyze spatial changes.