Designing and implementing effective monitoring and evaluation (M&E) is an integral element of wheat flour fortification programs. This review provides practical guidance for designing a M&E system for a flour fortification program. The Centers for Disease Control and Prevention's Framework for Program Evaluation in Public Health has been adapted to identify key issues in the development of an integrated M&E system. A clear understanding of 1) the stakeholders in flour fortification and their needs, 2) the description and context of the fortification program, 3) the country's wheat flour and flour products market, and 4) the resources available for the M&E component are critical and should be considered early in a program's design.