Periodontal ligament-associated protein-1 (PLAP-1) is an osteogenisis negative regulatory gene that inhibits the differentiation of rat bone marrow stromal cells (rBMSCs) into osteoblasts in vitro. The aim of this study was to verify whether PLAP-1 acted as an inhibitory factor of rBMSCs in rat critical-size skull defect repair in vivo. Six-week old male Wistar rats treated with a drill-hole injury were randomly assigned into five groups PLAP-1-transfected rBMSC group, empty vector-transfected rBMSC group, normal rBMSC group, collagen group and blank control group according to the treatment factors. Skull specimens were obtained at 8 weeks after surgery. X-ray examination, histological observation of hard tissue slices (HE, Masson staining and von Kossa staining), immunohistochemical staining were applied to evaluate the repair effects. X-ray examination showed that repair effect of the PLAP-1-transfected rBMSC group was significantly worse than that of the empty vector-transfected rBMSC group and normal rBMSC group. In HE staining, regenerated bone could only be observed in the partial defect area of the PLAP-1-transfected rBMSC group. However, new bone filled nearly the entire defects in the empty vector-transfected rBMSC group and normal rBMSC group. Mineralization of new bone in the two groups was significantly higher than that of the PLAP-1-transfected rBMSC group, according to Masson and von Kossa staining. Meanwhile, the transfected PLAP-1 gene worked well in vivo. Positive expression of PLAP-1 protein was only distributed in the newly formed bone of the PLAP-1-transfected rBMSC group, no positive staining was observed in the other four groups. Overexpression of PLAP-1 in rBMSCs inhibits new bone formation and mineralization in rat critical-size skull defects in vivo.