OBJECTIVE: This prospective clinical study aims to determine the differences between two treatment modalities for anterior open bite in growing patients. The treatment modalities involved the use of magnetic bite-blocks (MBBs) or rapid molar intruders (RMIs) applied with posterior bite-blocks. METHODS: Fifteen consecutive patients with a mean age of 11.2 (standard deviation [SD] = 1.6) years and a mean open bite of -3.9 mm were treated with MBBs. Another 15 consecutive patients with a mean age of 10.9 (SD = 1.8) years and a mean open bite of -3.8 mm were treated with RMIs applied on bite-blocks. Cephalometric radiographs were obtained before (T1) and immediately after appliance removal (T2). The treatments lasted four months, during which the appliances were cemented to the teeth. The morphological changes were measured in each group and compared using logistic regression analysis. RESULTS: The MBB group exhibited significantly greater decreases in SNA angle, ANB angle, overjet, and maxillary incisor angle (p < 0.05). The MBBs induced greater effects on the maxilla and maxillary dentition. The MBBs restrained maxillary forward growth and retracted the maxillary incisors more effectively than did the RMIs. Consequently, changes in the intermaxillary relationships and overjets were more distinct in the MBB group. CONCLUSIONS: The anteroposterior differences between the appliances suggest that MBBs should be preferred for the treatment of patients with Class II open bites and maxillary incisor protrusions.