Patient-specific cutting guides are used for safe and accurate jaw resection during oral and maxillofacial surgery. This study investigated the effect of shavings from 3D-printed cutting guide materials during surgery on bone healing. The biocompatibility of commercially available biocompatible polymers including photopolymer resin (PP) and polyamide resin (PA) materials was assessed in the present study. The viability of mouse osteoblast-like MC3T3E-1 cells was evaluated upon coculture with the materials. Furthermore, the effects of PP and PA as additives on bone formation were investigated in a rat calvarial bone defect model. Both PP and PA were biocompatible and allowed cells to attach to them. However, both materials could be damaged when cutting devices were used, and their shavings impaired osteoblast proliferation and bone formation. Cutting guide materials are designed to be biocompatible when they are fabricated according to the manufacturer’s protocol. Nevertheless, the polymer shavings generated during jaw cutting might adversely affect bone healing.