Brazilian Amazonia covers around 5 million km². If we could sample it regularly, with one sample for each 1 degree cell (10.000 km²), we would need 500 sample sites. It is clear that financial costs limit the amplitude of biodiversity studies. As the area to be explored is so large, financial resources limited, and demands varied, a program on Amazonian biodiversity research must be cost-effective. Integrated and large-scale studies, using standardized protocols represent the only way to achieve these goals. In this review, we report on experience gathered at two model sites in Amazonia, Reserva Ducke and Alter do Chão, which were used to design the Inventory Component of the Program on Biodiversity Research (PPBio) of the Brazilian government (http://ppbio.inpa.gov.br). We address the following issues:  1) how scale, size, shape and distribution of sampling units affect the outcome of biodiversity studies, in terms of the estimation of biotic complementarity between sites, estimation of organismal abundance, and modeling of species distributions; 2) how different sampling needs, from different taxonomic groups, can be adjusted in integrated protocols; 3) how costs can be reduced through sub-sampling. Use of the method in other research sites in Amazonia is being conducted successfully, and a large network of standardized plots is being constructed (see http://ppbio.inpa.gov.br). We also show that the PPBio design can be integrated into other methodologies currently used in large-scale biodiversity studies.