In this work we present and discuss the results of a novel and timely GPR-2D and GPR-3D survey performed at an archaeological rock shelter site, Lapa do Santo, localized in the karstic region of Lagoa Santa, central Brazil. A total of 113 ground-penetrating radar profiles were acquired with 200MHz and 400MHz shielded antennas aiming in identifying geological and archaeological anomalies in order to assist archaeologists in an excavation program. The GPR results indicated clear geophysical anomalies characterized by hyperbolic reflections and areas with high amplitude sub-horizontal electromagnetic waves. The anomalies observed by GPR were confirmed by the excavation of test units, allowing the identification anthropogenic features such as a fire-hearth structure and wooden artifact, and natural features, such as, tree roots and rocky bodies such as speleothems, boulders and bedrock. The results showed the efficiency of GPR method in identifying potential buried archaeological targets in cave sites within a karstic area, and they oriented to archaeological excavations, reducing costs and increasing the probability of finding archaeological targets in the initial stages of a project.