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Background: The global health system has a large arsenal of interventions, medical products and technologies to address current global health challenges. However, identifying the most effective and efficient strategies to deliver these resources to where they are most needed has been a challenge. Targeted and integrated interventions have been the main delivery strategies. However, the health system discourse increasingly favours integrated strategies in the context of functionally merging targeted interventions with multifunctional health care delivery systems with a focus on strengthening country health systems to deliver needed interventions. Neglected Tropical Diseases (NTD) have been identified to promote and perpetuate poverty hence there has been global effort to combat these diseases. The Neglected Tropical Diseases Programme (NTDP) in Ghana has a national programme team and office, however, it depends on the multifunctional health delivery system at the regional and district level to implement interventions. The NTDP seeks further health system integration to accelerate achievement of coverage targets. The study estimated the extent of integration of the NTDP at the national, regional and district levels to provide evidence to guide further integration. Methodology/Principal Findings: The research design was a descriptive case study that interviewed key persons involved in the programme at the three levels of the health system as well as extensive document review. Integration was assessed on two planes—across health system functions–stewardship and governance, financing, planning, service delivery, monitoring and evaluation and demand generation; and across three administrative levels of the health system–national, regional and district. A composite measure of integration designated Cumulative Integration Index (CII) with a range of 0.00–1.00 was used to estimate extent of integration at the three levels of the health system. Service delivery was most integrated while financing and planning were least integrated. Extent of integration was partial at all levels of the health system with a CII of 0.48–0.68; however it was higher at the district compared to the national and regional levels. Conclusions/Significance: To ensure further integration of the NTDP, planning and finance management activities must be decentralized to involve regional and district levels of the health system. The study provides an empirical measure of extent of integration and indicators to guide further integration. [ABSTRACT FROM AUTHOR]