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Introduction Community values and preferences should inform risk communication during pregnancy in the context of an epidemic of an emerging pathogen, given the high levels of uncertainty in the diagnosis and the probability of an adverse outcome.Methods We conducted a multicountry qualitative study with 98 women from 7 sites in Brazil, Colombia and Puerto Rico to understand their preferences for learning about Zika virus test results amid high levels of uncertainty in diagnostic testing and related outcomes. We used thematic analysis with a combined deductive and inductive approach to analyse findings from the in-depth interviews.Findings Across sites and time periods, women wanted to learn about their test results, the risk to their pregnancy or infant and the related uncertainty as early as possible. They wanted to separate risk communication from decision-making around the following steps to give them time to consider the test results, related risks and available services.Conclusions Communication of the risk associated with an emerging pathogen suspected to affect pregnancy and developmental outcomes is a fraught issue. Public health authorities and healthcare providers should work closely together to understand families’ preferences for risk communication in the presence of uncertainty and develop a community-informed plan for risk communication as early as possible during an epidemic of an emerging infectious disease.