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Electronic documentation systems have become integral to improving the quality of healthcare, reducing medical errors, and advancing the delivery of evidence-based medical care. A smooth transition from paper charting to an electronic documentation system is challenging. Using quality improvement tools and building on the clinical microsystems concept can assist with a smooth transition. Specific strategies include involving all stakeholders in the development and implementation of the plan, assessing the culture of the department, and identifying processes and patterns that require attention. Specific steps include developing a statement of aim, formulating a specific path to reach the aim, evaluating the progress of implementation, and creating a template for future process improvement. This article describes the process used in one midwestern NICU to implement an integrated electronic documentation system using a clinical microsystems approach and quality improvement methods. Challenges encountered and lessons learned are discussed.