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Distance sampling methods to estimate population densities are in wide use; however, this method may not be suitable for certain species or in certain habitats. Although validation of population estimates derived from distance sampling is necessary to determine the reliability of population estimates, validation is lacking in most studies. We measured densities of six lizard species, with particular emphasis on the endemic Dunes Sagebrush Lizard (Sceloporus arenicolus) at 14 sites throughout the range of this species in the Mescalero Sands ecosystem in southeastern New Mexico. We tested the accuracy of distance sampling by comparing results from 238 distance line transects to densities measured in 20 total removal plots. Density estimates from the distance sampling method (N = 238 transects) for S. arenicolus and all lizard species combined were 4.6 lizards/ha and 26.14 lizards/ha, respectively. Density estimates from the total removal plots (N = 20) were 30.0 lizards/ha for S. arenicolus and 85.0 lizards/ha for all lizard species combined. It is clear that, even in the relatively open shinnery oak sand dune habitat, distance sampling methods were not reliable and underestimated the densities of lizards. The disparity in density estimates from distance sampling versus total removal plots was caused by violation of the assumption of perfect detection of individuals on the transect line. Individuals that were unavailable for detection greatly influenced the density estimates. Because of the difficulty in correcting for biases, we suggest that distance sampling is not an appropriate sampling method for estimating densities of lizards.