Abstract: The detection of protein-protein interactions through two-hybrid assays has revolutionized our understanding of biology. The remarkable impact of two-hybrid assay platforms derives from their speed, simplicity, and broad applicability. Yet for many organisms, the need to express test proteins in S. cerevisiae or E. coli presents a substantial barrier, because variations in codon specificity or bias may result in aberrant protein expression. In particular, nonstandard genetic codes are characteristic of several eukaryotic pathogens, for which there are currently no genetically based systems for detection of protein-protein interactions. We have developed a protein-protein interaction assay that is carried out in native host cells, using GFP as the only foreign protein moiety, thus circumventing these problems. We show that interaction can be detected between two protein pairs in both the model yeast S. cerevisiae and the fungal pathogen C. albicans. We use computational analysis of microscopic images to provide a quantitative and automated assessment of confidence.