In this report, we investigated the accumulation of heavy metals in the lizard Microlophus atacamensis, in three coastal areas of the Atacama Desert, northern Chile. We captured reptiles in a non-intervened area (Parque Nacional Pan de Azúcar, PAZ), an area of mining impact (Caleta Palitos, PAL) and an active industrial zone (Puerto de Caldera, CAL). Our methods included a non-lethal sampling of reptiles' tails obtained by autotomy and a few sacrificed animals to perform a stomach contents analysis. The concentrations of lead, copper, nickel, zinc and cadmium were measured by atomic absorption spectrophotometry in both soil and prey and compared to those recorded in the lizards' tails. Data obtained from lizard tails captured in PAL showed significantly high concentrations of Pb, Cu, Ni, and Zn compared to the other two sites PAZ and CAL. We did not find statistically significant differences among PAZ, PAL and CAL soils, probably due to the similar geological composition of the sites. However, the regional background values for Pb indicate contamination or at least metal enrichment in soils of the three sites, for Cu the global background values indicate contamination for the three sites, and for Cd both the regional and global backgroud values show high values. The analysis of the stomach content showed differences in the food sources of the lizards among the sites studied. The concentration of heavy metal in lizard tissues versus prey delivered values of the Trophic Transfer Factor higher than one (1), suggesting that food may be a primary source of metals in the tissues of M. atacamensis. Calculations of the Bioaccumulation Factor (BAF) and the Ecological Risk (IR) resulted in values higher than one (1) indicating the relevance of this process in the sites studied. In this article, we report relationships between environmental contaminants, mainly putative preys, and concentrations found in lizard tails, which is more substantial in areas with historical heavy metal contamination such as PAL where the non-lethal technique developed in this research suggests a process of metal bioaccumulation in M. atacamensis.