Introduction The Botswana's Ministry of Health redesigned and adopted a new organizational structure in 2005, which was poorly implemented. This article explores factors that influenced the implementation of this organizational structure. Methods This article draws from data collected through in‐depth interviews with 54 purposively selected key informants comprising policy makers, senior managers and staff of the Ministry of Health (N = 40) and senior officers from various stakeholder organizations (N = 14). Findings Participants generally felt that the review of the Ministry of Health organizational structure was important. The previous structure was considered obsolete with fragmented functions that limited the overall performance of the health system. The new organizational structure was viewed to be aligned to current national priorities with potential to positively influence performance. Some key weaknesses identified included lack of consultation and information sharing with workers during the restructuring process, which affected the understanding of their new roles, failure to mobilize key resources to support implementation of the new structure and inadequate monitoring of the implementation process. Conclusion Redesigning an organizational structure is a major change. There is a need for effective and sustained leadership to plan, direct, coordinate, monitor and evaluate the implementation phase of the reform. Copyright © 2014 John Wiley & Sons, Ltd.