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Purpose: This article presents the rationale and design of the Mountain States Genetics Regional Collaborative Center's Metabolic Newborn Screening Long-Term Follow-up Study. Methods: This study is a collaboration of multi-site metabolic providers throughout the Mountain States region investigating the long-term outcomes of individuals with metabolic conditions detected by newborn screening. Results: The Mountain States Genetics Regional Collaborative Center's Metabolic Consortium developed disease-specific care plans that included baseline and follow-up datasets for all metabolic disorders detected by both standard and tandem mass spectrometry newborn screening. Conclusion: These disease-specific care plans are used at multiple metabolic clinics throughout the Mountain States region. The shared datasets consisting of both performance and outcome indicators will be used to explore questions related to the treatment and outcome of these rare metabolic disorders. They will be used to assess the impact of newborn screening by comparing those individuals detected by newborn screening with those individuals diagnosed clinically, therefore allowing the systematic investigation of factors that impact long-term outcome.