On the Pacific island of Guam, control of the invasive Brown Treesnake (Boiga irregularis) relies largely on methods that use mice as bait. Juvenile B. irregularis feed primarily on lizards and their eggs, but little is known about their prey preference. We conducted an experiment to investigate preferences for, and acceptance of, dead geckos, skinks, and neonatal mice, in juvenile B. irregularis ranging from 290 mm to ca. 700 mm snout-vent length (SVL). Snakes of all sizes showed a preference for geckos over skinks and neonatal mice. Geckos were the first prey chosen in 87% of 224 initial trials (56 snakes subjected to four trials each; 33% would be expected from a random choice). The smallest snakes had the most pronounced preference. Although many of the snakes accepted neonatal mice and/or skinks, some snakes of all sizes were reluctant to feed on anything but geckos, especially when well fed. We also addressed the hypothesis that repeated encounters with a particular prey type increase a snake's preference for that prey. Our study does not support this hypothesis. Our results suggest that control methods relying solely on rodent bait may be inefficient for targeting snakes < 700 mm SVL and that individual heterogeneity in prey preference may cause a significant part of this juvenile cohort to be completely refractory to capture with rodent bait, even if the bait is dead and small enough to be readily swallowed.