Objective: To describe and analyze the use and costs of hospital services for children diagnosed with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency either with newborn screening or clinical diagnosis in Australia between 1994 and 2002. MCAD deficiency is a potentially lethal disorder of fatty-acid oxidation. Study design: We conducted a retrospective audit of medical records supplemented by a parental survey. Results: A total of 59 children with MCAD deficiency were identified, 24 by using newborn screening. In the first 4 years of life, screening children cost an average of $A1676 (US$1297) per year for inpatient, emergency department, and outpatient visits, compared with $A1796 (US$1390) for children in whom a clinical diagnosis was made. Forty-two percent of the children who underwent screening were admitted to the hospital, compared with 71% of children who did not undergo screening. Children who did not undergo screening used significantly more inpatient services and cost significantly more in emergency services. There were also some significant differences in use on a year-by-year basis. Conclusions: Children who do not undergo screening may be more likely to be admitted to the hospital and to incur higher emergency department costs than children who underwent screening, and children seem more likely to attend hospital outpatient clinics. Screening does not result in higher costs from a hospital perspective.