Objective: To compare the effects of mineral trioxide aggregate (MTA) and calcium hydroxide (CH) for pulpotomy in primary molars. Methods: A randomised, bilateral self-controlled clinical trial was designed to compare the clinical effect of MTA and CH in pulpotomies in primary molars in 4- to 9-year-old children. Children with two similar-sized cavities on bilateral primary molar counterparts requiring pulpotomies were included. The two contralateral molars in each patient were randomly assigned to MTA or CH treatment. Clinical and radiographic examinations were performed to evaluate the treatment results at post-treatment recall. Results: Seventeen pairs of self-controlled contralateral teeth were available for follow-up evaluations. The success rate of MTA was 94.1% (16/17), while the success rate of CH was 64.7% (11/17). Internal root resorption was the most frequent reason for failure in the CH group. Crown discolouration was common in the MTA-treated group. Conclusion: MTA was more successful than CH for pulpotomies in primary molar teeth, and may be a suitable replacement for CH in primary molar pulpotomies. Keywords: calcium hydroxide, internal root resorption, mineral trioxide aggregate, primary molars, pulpotomy