We assessed the health status of chimpanzees (Pan troglodytes schweinfurthii) of the Kanyawara group in the Kibale National Park in Western Uganda via noninvasive methods. We conducted visual veterinary inspection, parasitological and urine analysis in association with behavioral observations, causing minimal disturbance or stress to individually recognized chimpanzees. We applied multiple parasitological techniques to 252 stool samples to compare their efficacy in detecting parasitic infection and to increase the power of detecting a wide range of parasites at a more sensitive level. We examined 76 urine samples via a quick detection method to evaluate multiple parameters of urine that indicate organ dysfunction. Results of the different analyses are mutually supportive and provided useful information for monitoring bodily condition and diseases. The multifaceted health evaluation system is a beneficial tool for monitoring long-term and short-term changes in health status due to environmental stress, seasonal dietary change, and disease in wild chimpanzee populations. Use of this method to detect changes in health, when employed together with behavioral observations, may also provide important insights into the potential effects of self-medicative behaviors.