Whole exome sequencing (WES) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Stratification of individual's ethnicity is fundamental for the correct interpretation of personal genomic variation impact. We implemented EthSEQ to provide reliable and rapid ethnicity annotation from whole exome sequencing individual's data and validated it on 1,000 Genome Project and TCGA data demonstrating high precision (>99%). EthSEQ can be integrated into any WES based processing pipeline and exploits multi-core capabilities. Source code, manual and other data is available at http://demichelislab.unitn.it/EthSEQ.