To improve our understanding of the distribution and abundance of amphibians and reptiles in tropical forests, herpetologists need to understand the relative effectiveness of different sampling techniques. However, current studies are biased by a focus on certain methods, species groups, or geographic regions. To address this problem, we conducted the first standardized comparison of patterns of species richness, rank-abundance, and community structure for both passive and active sampling methods for the study of herpetofauna in a tropical forest landscape. Moreover, we compare the effectiveness of these methods in primary and secondary forests and Eucalyptus plantation. Although different methods captured significantly different numbers of species and individuals, almost all techniques provided complementary benefits for the sampling of both lizards and leaf litter amphibians. The use of a limited set of methods can severely bias our understanding of changes in amphibian and lizard community structure in response to large-scale habitat change. Contrary to other studies, we recommend the use of pitfall traps in all studies, even Rapid Assessments (RAP), because they are indispensable for sampling many cryptic species, as well as being particularly cost effective for large-scale research. Because of the combination of complementary methods in sampling effectiveness, and the influence of method choice on taxon responses to habitat change, we recommend the use of multiple sampling techniques wherever possible. Synchronous adoption of multiple techniques in field studies will help improve sample representation and, thus, the understanding of species distributions and human impacts on herpetofauna in tropical forests.