Between June 1998 and January 2000, "The Master Plan Study on Strengthening Primary Health Care Services (JICA PHC Study)" was executed in the Republic of Malawi. The purpose of the study was to formulate a central region master plan and a national master plan to improve the primary health care (PHC) system, and to transfer essential research, analytical skills, and methodologies to Malawian counterparts. The health investigations covered the referral system, human resources, health finance, policy and management, the health management information system, community participation, logistics systems and health facilities and supplies. As a result of the study, childhood malnutrition, maternal health, and the inappropriate role of informal drug-sellers, in the PHC system were found to be key health issues, and on the basis of these problems the national master plan was formulated with six prioritized proposed projects. In this report, the following challenges to the execution of effective and efficient study were discussed and recommended through the review of health development studies conducted in five developing countries including Malawi; 1) the study purpose and the concept of a master plan should be clarified, 2) the study outcome should be evaluated and utilized effectively, 3) terms of reference for the study should be reviewed and improved, 4) a better relationship with counterparts and donors should be developed, and 5) a capacity of participants in the study such as consultants should be built up.