BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes the haplotypes of 32xe2x80x89488 samples across 39.2 million SNPs into a 7.4 GB database and decodes up to 420 million genotypes per CPU second. The high performance enables real-time responses to complex queries.