Whole exome sequencing (WES) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Stratification of individuals 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 individuals data, validated it on 1000 Genome Project and TCGA data (2700 samples) demonstrating high precision, and finally assessed computational performances compared to other tools. EthSEQ can be integrated into any WES based processing pipeline and exploits multi-core capabilities.