The authors describe a conceptual and measurement framework that provides a template for guiding policy development and systems change. The framework is built on the concepts of vertical and horizontal alignment, system-level processes, and organization-level practices. Application of the framework can structure the thinking and analytic activities of systems and organization-level personnel and can help them identify significant disconnects between and among system-level processes and organization-level practices. Once the disconnects are identified, information can be used to develop policies that enhance the alignment or congruence between system-level processes and organization-level practices, or implement systems changes that enhance the logical sequence of input and throughput, input and output, and/or throughput and output program logical components. The article concludes with a discussion of a number of change-oriented principles (vision of the future, simple communication, leadership, empowering, immediate feedback and reinforcement, organization's culture) and guidelines (pace the change process, reallocate and restructure resources, alignment process, partnerships, continuous quality improvement framework, system and organization-level outputs, innovation, performance-based evaluation and management system) that address significant challenges faced today by intellectual and developmental disabilities' organizations and systems.