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This study aimed to quantify the microdamage to cortical bone of different thickness and the maximum insertion torque during orthodontic miniscrew implant (OMI) placement with and without a pilot hole. Forty-five porcine bone specimens were prepared with thicknesses of 1.5, 2 and 2.5 mm. Ten bone specimens per thickness had a pilot hole drilled prior to the insertion of an OMI, and the remaining 15 bone specimens had an OMI without a pilot hole inserted. Sequential staining was used to identify damage caused by bone preparation and surface microdamage from OMI insertion and confocal laser microscopy images were used to quantify damage characteristics. Of the five damage characteristics, only one decreased when a pilot hole was used for all bone specimens (p = 0.025), while two increased as cortical bone thickness increased (p = 0.0064, p = 0.0003). There was no evidence that maximum insertion torque differed according to pilot hole status (p = 0.1144) and increased as cortical bone thickness increased (p = 0.0001). The presence of a pilot hole had minimal effect on microdamage characteristics and no effect on maximum insertion torque. As cortical bone thickness increased, an increase in microdamage and in maximum insertion torque was observed.