The two-hybrid method detects the interaction of two proteins by their ability to reconstitute the activity of a split transcription factor, thus allowing the use of a simple growth selection in yeast to identify new interactions. Since its introduction about 15 years ago, the assay largely has been applied to single proteins, successfully uncovering thousands of novel protein partners. In the last few years, however, two-hybrid experiments have been scaled up to focus on the entire complement of proteins found in an organism. Although a single such effort can itself result in thousands of interactions, the validity of these high-throughput approaches has been questioned as a result of the prevalence of numerous false positives in these large data sets. Such artifacts may not be an obstacle to continued scale-up of the method, because the classification of true and false positives has proven to be a computational challenge that can be met by a growing number of creative strategies. Two examples are provided of this combination of high-throughput experimentation and computational analysis, focused on the interaction of Plasmodium falciparum proteins and of Saccharomyces cerevisiae membrane proteins.