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During the austral spring of 2013 GPR measurements were performed with an airborne instrument over glaciers of the semi-arid high Andes of central Chile (latitude 33 degrees S). We describe the instrumentation of the 50 MHz pulse radar, the method, and the results of ice thickness and internal stratigraphy. One of these glaciers, Juncal Norte, reaches an altitude of almost 6000 m, the glacier at Volcan Tupungatito starts at 5750 m. The comparison of ground based and airborne measurenments proves the accuracy of the airborne method and particularly the advantage of performing fast measurements covering large areas in a fraction of the time otherwise needed with ground studies. To our knowledge these are the highest elevation airborne GPR data acquired to date.