The Stout Iguana (Cyclura pinguis) is a critically endangered species endemic to the Puerto Rico Bank and currently restricted to the British Virgin Islands (BVI). Our study on Guana Island, BVI, focused on vertical structure use. Based on previous incidental observations, we hypothesized that Stout Iguanas use vertical structures and that adults and juveniles use such structures differently. In October 2011, we documented movement and vertical structure use by adult (n = 4) and juvenile (n = 11) iguanas with tracking bobbins. We recorded structure types used, heights attained on structures, distances between structures, and structure sizes. We found that Stout Iguanas used vertical structure more than previously documented. Trees comprised a significantly greater (P < 0.001) proportion of structures used by juveniles than by adults, whereas rocks comprised the greatest proportion of structures used by adults. In addition to differential structure use, juveniles climbed significantly higher (2.4 vs. 0.9 m on average; P < 0.001) than adults. We found no difference in the diameter or distance between structures used by adults and juveniles. Our results suggest that vertical structure use may be an important habitat element for free-ranging juvenile Stout Iguanas. Habitat management that provides vertical structure may be advantageous for the conservation of this species.