During orthodontic therapy, patients frequently complain about pain and discomfort, especially during insertion of fixed appliances. Skeletal anchorage using an interdental microimplant is a new concept in orthodontic treatment. The purpose of this study was to investigate differences and changes in the level of pain among patients in relation to orthodontic microimplant treatments. Forty microimplants were applied to the maxilla as skeletal anchors in the orthodontic treatment. The visual analog scale (VAS) was used to evaluate the patients' perception of pain during this new modality treatment. The premolar extraction VAS core was used as a baseline for the complete orthodontic procedure. The mean VAS score was 35.8 mm at 24 h after premolar extraction. The mean VAS score for insertion and removal of the microimplant 24 h after the operation was 12.3 and 7.8 mm, respectively. Three months after removal of the skeletal anchors, the VAS score had decreased to 3.2 mm and was the same as with the traditional orthodontic treatment. By using the repeated-measure general linear model (GLM), we found that the score 1 day after microimplant placement was significantly less than that 1 day after first premolar extraction or that 1 day after fixed appliance insertion. This result indicates that interdental microimplant did not generate any greater pain than other orthodontic procedures. Therefore, patients were willing to adopt the new orthodontic treatment.