ABSTRACT Objectives: Micro-osteoperforation is a minimally invasive procedure to accelerate orthodontic tooth movement. Accelerated orthodontics can sometimes lead to migration of the anchor teeth. The objective of this randomised control study was to compare the amount of mesial molar migration between different depths (3 millimetre and 6 millimetre) of micro-osteoperforation assisted canine retraction. Methods: Ten adult patients requiring extraction of maxillary first premolar for orthodontic treatment were enrolled for this split mouth study. The micro-osteoperforation of varying depth (3 millimetre and 6 millimetre) were made using a mini implant. Direct anchorage was taken with the help of a mini implant to retract the canine teeth. The patients were divided into two groups - 3 millimetre depth and 6 millimetre depth of micro-osteoperforation. The primary outcome was to compare the mean mesial molar migration between the two groups for three months. Results: The mean mesial molar migration with 3 millimetre depth of micro osteoperforation was 0.49 ± 0.20 millimetre and with 6 millimetre depth it was 0.39 ± 0.18 millimetre, which was statistically insignificant (P >0.350). Conclusion: Micro-osteoperforations of different depths do not cause a significant difference in mesial molar migration and are not clinically significant. When it comes to clinical situations even a slight mesial movement of molar can have high significance in the treatment outcome.