Purpose of reviewAs more genomes are sequenced, the difficult task of characterizing the gene products of these genomes becomes the compelling mission of biological sciences. The melding of whole organ physiology with transgenic animal models, gene transfer methods and RNA silencing promises to form the next wave of scientific inquiry. A host of new microscopy imaging technologies enables researchers to directly visualize gene products, probe alterations in cell function in transgenic animals and map tissue organization. This review will describe these microscopy imaging techniques, their advantages, imaging properties and limitations.Recent findingsNew optical methods such as two-photon confocal microscopy, fluorescence resonance energy transfer, and total internal fluorescence reflectance microscopy are increasingly being applied to extend our understanding of whole organ and renal epithelial function. Two-photon confocal microscopy has been used to image directly into the kidney of living animals. Fluorescence resonance energy transfer has been used to directly visualize transcription factor complexes within the nucleus while total internal fluorescence reflectance microscopy has permitted direct observation of protein delivery to the plasma membrane.SummaryThe application of these optical techniques along with the ability to label virtually any protein with a fluorescent tag will enable researchers to study cellular processes and whole organ functionin vivo. Light microscopy methods will allow an advance from semi-quantitative to quantitative approaches to problems of relevance to physiologists studying issues related to renal function.