The perinatal periods of risk (PPOR) methods provide a framework and tools to guide large urban communities in investigating their feto-infant mortality problem. The PPOR methods have 11 defined steps divided into three analytic parts: (1) Analytic Preparation; (2) Phase 1 Analysis-identifying the opportunity gaps or populations and risk periods with largest excess mortality; and (3) Phase 2 Analyses-investigating these opportunity gaps. This article focuses on the Phase 2 analytic methods, which systematically investigate the opportunity gaps to discover which risk and preventive factors are likely to have the largest effect on improving a community's feto-infant mortality rate and to provide additional information to better direct community prevention planning. This article describes the last three PPOR epidemiologic steps for investigating identified opportunity gaps: identifying the mechanism for excess mortality; estimating the prevalence of risk and preventive factors; and estimating the impact of these factors. While the three steps provide a common strategy, the specific analytic details are tailored for each of the four perinatal risk periods. This article describes the importance, prerequisites, alternative approaches, and challenges of the Phase 2 methods. Community examples of the methods also are provided.