Whey acidic protein (WAP) has been identified in a wide range of species as a major whey protein in milk. Our previous studies have shown that the mouse WAP inhibits the proliferation of mammary epithelial cells, and has a function of reducing tumorigenesis and invasion of MCF-7 cells derived from human breast cancer. In some species including humans, however, WAP is not synthesized in the mammary gland. In this study, to investigate an available use of human WAP as a biological substance, we restored the nonfunctional human WAP gene and analyzed its function. Comparative DNA database analysis of the nonfunctional human WAP gene with known WAP genes confirmed the presence of critical nucleotide substitutions, deletion and insertion within the coding region of human WAP gene. The nucleotide mutations (three points) were restored using a site-directed mutagenesis system (Invitrogen, CA, USA). DNA sequencing showed that the nonfunctional human WAP gene was successfully restored. Transfection of the restored human WAP gene into MCF-7 cells induced a significant decrease in their proliferating and invasive abilities. The human WAP-expressing MCF-7 cells also showed a significant decrease in tumorigenesis in nude mice after the subcutaneous transplantaion. The present study demonstrated that the restored human WAP gene displayed its biological function.