Objective To detect the expression of alkaline phosphatase(akp) mRNA in in vivo tissue engineering bone constructed with calcium phosphate cement and do a comparison with that in naturally healing bone. Methods 28 porous calcium phosphate cement cylinders were implanted into the dorsal muscles of 7 dogs respectively and one molar was pulled out in each dog to create naturally healing bone model. The in vivo tissue engineering bone and the naturally healing bone were harvested at 3/7, 1, 2, 4, 8, 12 and 24 weeks post-implantation. Then, akp mRNA was detected by real-time quantitative polymerase chain reaction(PCR). Results In this experiment akp mRNA was expressed at lower levels with delayed peak in in vivo tissue engineering bone than that in naturally healing bone. However, the expression of akp mRNA shared a similar pattern of initially upregulated and finally down-regulated in the two kinds of bone. Conclusion The in vivo tissue engineering bone is calcified later and fewer than natrually healing bone. However, the gene expression pattern is similar to that of naturally healing bone in bone formation.