Background: Studies evaluating development of health information systems in developing countries are limited. Most of the available studies are based on pilot projects or cross-sectional studies. We took a longitudinal approach to analysing the development of Botswana’s health information systems.

Objectives: We aimed to: (i) trace the development of the national health information systems in Botswana (ii) identify pitfalls during development and prospects that could be maximized to strengthen the system; and (iii) draw lessons for Botswana and other countries working on establishing or improving their health information systems.

Methods: This article is based on data collected through document analysis and key informant interviews with policy makers, senior managers and staff of the Ministry of Health and senior officers from various stakeholder organizations.

Results: Lack of central coordination, weak leadership, weak policy and regulatory frameworks, and inadequate resources limited development of the national health information systems in Botswana. Lack of attention to issues of organizational structure is one of the major pitfalls.

Conclusion: The ongoing reorganization of the Ministry of Health provides opportunity to reposition the health information system function. The current efforts including development of the health information management policy and plan could enhance the health information management system.