The workshop ‘ Species distribution models: applications, challenges and perspectives ’ held at Belo Horizonte (Brazil), 29–30 August 2011, aimed to review the state-of-the-art in species distribution modelling (SDM) in the neotropical realm. It brought together researchers in ecology, evolution, biogeography and conservation, with different backgrounds and research interests. The application of SDM in the megadiverse neotropics—where data on species occurrences are scarce—presents several challenges, involving acknowledging the limitations imposed by data quality, including surveys as an integral part of SDM studies, and designing the analyses in accordance with the question investigated. Specific solutions were discussed, and a code of good practice in SDM studies and related field surveys was drafted.