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In this data article, we investigated the accumulation of heavy metals in the lizard Microlophus atacamensis, in three coastal areas of the Atacama Desert, northern Chile. We captured lizards in a non-intervened area (Parque Nacional Pan de Azucar, 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 lizard's tails obtained by autotomy. The concentrations of lead, copper, nickel, zinc and cadmium were measured in both soil and prey and