The main goal of total disc replacement (TDR) is to preserve motion. Despite reports of good clinical outcomes, various degrees of heterotopic ossification after TDR have been reported. The purpose of this study was to investigate the prevalence and its clinical relevance of heterotopic ossification. We evaluated 65 consecutive patients (82 segments) with mean follow-up duration of 45 months (range, 12-88 months). Two kinds of prosthesis, ProDisc® for 75 segments (91.5%) and CHARITE™ for seven segments (8.5%), were used. Patients with heterotopic ossification were compared with those without heterotopic ossification with regard to segmental flexion-extension ROM, VAS and ODI. We analysed the occurrence site by nine zones. Heterotopic ossification was detected in 25 out of 82 segments (30.5%) at a mean follow-up of 17 months. According to McAfee's classification, there was Class-I heterotopic ossification in eight segments (9.8%), Class-II in 12 segments (14.6%), and Class-III in five segments (6.1%). There was no Class-IV heterotopic ossification. There were no significant differences in the segmental ROM, VAS and ODI between the patients with Class-I or Class-II heterotopic ossification and those without heterotopic ossification The segmental ROM in the patients with Class-III heterotopic ossification was significantly decreased compared with the patients without heterotopic ossification (p = 0.018). But VAS and ODI were not significantly different compared with those of patients with no heterotopic ossification. Most heterotopic ossification (82.5%) was detected in the anterior and posterior aspects. In conclusion, most of the heterotopic ossification (Classes I and II) did not affect segmental ROM and clinical outcomes such as pain or function. In Class-III heterotopic ossification segmental ROM was decreased, but it did not affect clinical outcomes.