During the past decade, indicators for the assessment, monitoring, and evaluation of services provided by humanitarian organizations to populations affected by complex emergencies (CEs) were developed to improve the effectiveness and accountability of humanitarian response. The quality of data used to develop individual indicators and their relationship to positive health outcomes varies greatly. This article states the essential characteristics necessary for the development and implementation of effective indicators in CE response and proposes the establishment of an evidence-based grading system. The importance of trend analysis and the modification or addition of various indicators and their thresholds, according to phase and location of CEs, are stressed. Limitations in the development, implementation, and interpretation of these indicators, including those outside of the organizations' control are discussed. More evidence-based research is needed as to the type and thresholds of indicators that lead to improved health outcomes in populations affected by CEs. The use of indicators by non-governmental organizations, and how they affect their program's decision-making in different phases and settings within CEs need further study. Finally, the establishment of a regulating body with the authority to enforce the attainment of standards by use of these indicators is necessary to avoid inappropriate humanitarian assistance causing loss of life in the future.