A common method for urine collection from rats requires the use of a metabolic cage, thus exposing animals to extended periods of isolation in an unfamiliar cage with a wire-mesh floor. A new method involving hydrophobic sand, a material more similar to bedding, has become available recently but has not been extensively compared with metabolic cages in regard to collection efficiency or stress. Using a within-subjects crossover design, we examined differences in stress markers, urinary markers, and urine volume of clinically healthy male Sprague-Dawley rats during 2-, 4-, and 6-h collection sessions in hydrophobic sand and metabolic cages. Stress response markers of weight loss, fecal pellet output, or corticosterone did not differ between hydrophobic sand and metabolic cages, and observed behavior suggested that sand may be less stressful than metabolic cages. All clinically relevant urinary markers examined were normal, with no differences between collection methods. Total urine volume collected was greater from the metabolic cage than sand in 3 of the 5 sessions, but the volume collected during the shortest session (2 h) did not differ between methods and accounted for 62% of the total volume collected during the longest session (6 h). Our results suggest that hydrophobic sand is a refinement of urine collection methods for rats that decreases isolation time, risk of injury, and stress and maintains the integrity of urine samples.