The ability to measure body composition is critical for studying the physiological ecology of animals. This is particularly true for small mammals that have a high metabolic rate. We evaluated a nondestructive method of body composition analysis that would allow accurate assessment of body fat, body water, and lean mass. We used total body electrical conductivity (TOBEC) to estimate body composition in the little brown myotis (Myotis lucifugus). In a sample of 46 individuals, TOBEC was both accurate and precise in estimating total body water and lean mass but was less effective at estimating total body fat. Mass-independent or whole-body compartments (i.e., total body water, total body fat, lean dry mass, and lean body mass) were more accurately estimated than mass-dependent or mass-specific body composition compartments (i.e., water content, fat index, and % lean dry mass). The TOBEC measurements we made using an SA-3000 analyzer were influenced by extremes in body temperature, as well as by aluminum and incoloy wing bands. Our study also presents a new method of restraint especially suited for small mammals and birds that increases precision of TOBEC measurements. This study shows that TOBEC is a potentially valuable tool for studying changes in body composition of small mammals and may provide insight into the physiological impacts of various life history stages such as postnatal growth, reproduction, and hibernation.