Physiological and anatomical investigations are commonly combined in experimental models. When studying the lower urinary tract (LUT), it is often of interest to perform both urodynamic studies and retrogradely labeled neurons innervating the peripheral target organs. However, it is not known whether the use of anatomical tracers for the labeling of, e.g. spinal cord neurons may interfere with the interpretation of the physiological studies on micturition reflexes. We performed cystometry and external urethral sphincter (EUS) electromyography (EMG) under urethane anesthesia in adult female rats at 5-7 days after injection of a 5% fluorogold (FG) solution or vehicle into the major pelvic ganglia (MPG) or the EUS. FG and vehicle injections into the MPG and EUS resulted in decreased voiding efficiency. MPG injections increased the duration of both bladder contractions and the inter-contractile intervals. EUS injections decreased EUS EMG bursting activity during voiding as well as increased both the duration of bladder contractions and the maximum intravesical pressure. In addition, the bladder weight and size were increased after either MPG or EUS injections in both the FG and vehicle groups. We conclude that the injection of anatomical tracers into the MPG and EUS may compromise the interpretation of subsequent urodynamic studies and suggest investigators to consider experimental designs, which allow for physiological assessments to precede the administration of anatomical tracers into the LUT.