As a non-invasive approach for sampling small mammals, track tubes may be especially useful in species occupancy studies that do not require marking of individuals. However, such studies may involve significant uncertainty in identifying many tracks to species. Using 37 study sites in eastern Alabama and Tennessee, we compared relative differences in detection probabilities with track tubes vs. live traps for Peromyscus (deermice), Oryzomys palustris (Marsh Rice Rat), and Sigmodon hispidus (Hispid Cotton Rat). In analyses that ignored identification uncertainty or that used false-positive occupancy models to address this uncertainty, track tubes and live traps had similar detection probabilities. When uncertain detections were omitted from analysis, effective detectability was lower with track tubes. False-positive occupancy modeling indicated that track-identification uncertainty could not be ignored, as there was a non-zero probability of false-positive detections. False-positive occupancy designs have high relevance to track-tube studies; in addition, such studies should ensure that track identification is done under the oversight of an experienced tracker.