Objectives: To analyse the relevance and quality of the research proposals submitted to the 2016 call for proposals for the initiative Improving Programme Implementation through Embedded Research (iPIER-2016) to address current public health challenges in Latin America and the Caribbean. Methods: We performed a cross-sectional study using information from 108 research proposals using quantitative and qualitative methods. We used three frameworks to analyse the relevance of the proposals: The Global Burden of Disease, the WHO Health Systems Conceptual Framework and the Sustainable Development Goals proposed in 2015 by the United Nations. We performed an index to analyse the relevance and quality of the proposals. Results: Twenty seven percent of the proposals have very good relevance, one third of the proposals have quality flaws. This means their research questions are not related to implementation research or their methods are insufficient or inadequate to respond to the objective. Conclusions: The response to this call is proof of health authorities' interest in research as a tool to improve the implementation of health programs in the region. However, proposals show important variations in terms of relevance and quality among countries and training health staff in programme implementation seems a central requirement.