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Inborn error of metabolism (IEM) was very rare hereditary disease. Newborn screening by Tandem mass spectrometry (MS/MS) program which can detect 17 diseases of inborn error of metabolism has been introduced in Japan since 2011. The objective of this study was to estimate the incremental cost-effectiveness ratio (ICER) of the MS/MS tests compared with Guthrie (GC) tests. Methods: A costutility analysis was conducted. We constructed a decision-tree and Markov model to compare lifetime costs and quality-adjusted life-years (QALY). The comparisons were made between a current newborn screening program using MS/MS tests and a past screening program using GC tests. We conducted a systematic review to collect health benefits values. Treatment costs and disease progression rates were estimated using an administrative database in Japan. Disease prevalence and mortality rate were obtained from publications from government and Bulletin of the Japan Cooperative Project on Special Formula. Results: The ICER of MS/MS tests compared with GC tests was 2 million JPY per QALY (approximately $19,000 per QALY) which was lower than the willingness-to-pay threshold of 5 million JPY in Japan. Conclusions: Introduction of the new program with MS/MS tests has incurred additional costs to insurance payer; however, it has also yielded additional QALYs. Therefore, from the perspective of Japanese healthcare system, the MS/MS tests seemed to be cost-effective. However, the data of IEM such as incidence, transition probabilities, and utility, were limited, a long-term epidemiological study for the IEM patients is needed to reduce uncertainty of this analysis.

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