Background: Newborn screening (NBS) for cystic fibrosis (CF) has been underway universally in the USA for more than a decade, as well in most European countries, and algorithms have been evolving throughout this period with quality improvement projects as immunoreactive trypsinogen determinations alone have been transformed to a 2-tier strategy with DNA analyses. Objective: To apply next generation sequencing (NGS) as a method for expanding the DNA tier for identifying variants in the cystic fibrosis transmembrane conductance regulator ( CFTR) gene with minimization of unintended outcomes. Design: Sequential quality improvement project in three phases using plan coupled to statewide follow up and analysis of screening outcomes in comparison to other NBS programs that use CFTR sequencing. Results: After demonstrating feasibility in the first phase, we studied an IRT/NGS algorithm that included CFTR Variants with Varying Clinical Consequences (VVCCs). This revealed a high identification of CF patients with 2-variants detected through screening, but for every CF case there were 1.4 with cystic fibrosis metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID). This led us to a third phase of quality improvement in which the VVCCs were eliminated except for R117H, resulting in 94% 2-variant detection of patients and 0.44:1 ratio of CRMS/CFSPID to CF. Conclusion: NGS can be used with IRT as an effective method of identifying infants at risk for CF without an appreciable increase in detection of either carriers or CRMS/CFSPID cases.