In the past decade, tremendous progress has been made in understanding the molecular mechanisms that underlie many neurodegenerative disorders, and common aspects of the pathological processes that lead to neuronal cell death have emerged. Nearly all of these advances have come from genetic, molecular, and biochemical studies that point to alterations in protein folding or protein-protein interactions as the fundamental mechanism behind these disorders. New microscopy/imaging technologies for detecting protein-protein interactions are now poised to contribute to progress in this field. Here we describe a novel technique based on fluorescence resonance energy transfer, called fluorescence lifetime imaging microscopy (FLIM), which allows monitoring of protein conformation and protein-protein interactions in intact cells. For example, using FLIM, we have studied the interaction of two proteins related to Alzheimer's disease: amyloid precursor protein (APP) and presenilin (PS-1). By measuring the lifetime of a donor fluorophore linked to PS-1, we show, with high subcellular resolution, localization of the PS-1-APP interaction within neurons. This approach may have widespread applicability in studies of neurodegenerative disease mechanisms.