In 1977, the Ministry of Health and Welfare (MHW) directed prefectural officials in charge of maternal and child health to start publicly funded newborn mass-screening (NBS) for phenylketonuria (PKU), maple syrup urine disease (MSUD), histidinemia, homocystinuria and galactosemia and a study group of MHW formulated the treatment guideline for the target diseases. In 1980, MHW launched the Japan Cooperative Project on Special Formula (JCPSF) to ensure a stable supply of special formula and also organized the committee for JCPSF. From 1977 to 2003, a study group of MHW conducted a follow-up study of the patients detected by the screening. From the follow-up it was concluded that dietary therapy was unnecessary for histidinemia and the screening for the disease was discontinued. In 1995, the guideline for the treatment of PKU was revised to keep lower blood phenylalanine levels. The guideline committee for the treatment of BH4 deficiency was establish in 1996 to obtain better prognosis. In 2012, the MHW decided to initiate publicly funded NBS using MS/MS for inborn errors of amino acid, organic acid, and fatty acid metabolism. The Japanese nationwide NBS has been performed for 35 years. This paper reviews the Japanese history of the development of NBS which has enabled more IEM patients to lead active and productive lives today.