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We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAVusing eight experimentally validated “gold standard” positively selected variants and simulations. FineMAVhas good sensitivity and a low false discovery rate. Applying FineMAVto the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3and PRSS53associated with hair phenotypes that we validate using available independent data. FineMAVis widely applicable to sequence data from both human and other species.