Reports of severely malformed amphibians in the 1990s prompted researchers to examine the causes and extent of the issue. However, disparities in survey methods and a shortage of baseline data have hindered standardization among investigations. Here, we review field-based surveys and experimental approaches used over the last decade to address this complex ecological issue. We offer specific recommendations regarding amphibian-sampling techniques, including methods to capture and examine amphibians, with the aim of enhancing the accessibility of this topic to scientists, students, and educators of diverse backgrounds. Based on established approaches from epidemiology, we provide recommendations regarding methods to identify proximate causes(s) of abnormalities with a focus on using “multiple lines of evidence,” including large-scale field surveys, comparing malformation “signatures” between field and laboratory studies, and using of manipulative experiments at multiple spatial scales. As an example, we describe methods to examine the causal influence of infection by the trematode parasite, Ribeiroia ondatrae, including quantifying presence and abundance within amphibian and snail host populations with adequate power of detection. We conclude by identifying outstanding questions with the goal of stimulating additional research to evaluate the causes and consequences of amphibian malformations.