Large scale genotyping of a moderate number of loci is cost prohibitive with current chip-based technologies. We demonstrate the ability to use next generation sequencing technologies to genotype many DNA samples for a moderate number of loci – a mass genotyping by sequencing technology (MGST). Our MGST uses barcodes contained within probes as well as barcodes added by PCR to prepare a highly multiplexed library suitable for sequencing on the Illumina platforms. The cost per sample is highly competitive and will permit the routine genotyping of a moderate number of loci on a large number of samples. In six separate MGST experiments, with 24 loci on 24 to 96 B. taurus samples we have obtained 96% to 100% concordance with genotype data previously identified using the Illumina BovineSNP50 bead chip. In another MGST experiment with a different set of 54 loci on 96 B. taurus samples, we achieved 96% concordance. We are currently testing probe panels with 113 separate loci. USDA is an equal opportunity provider and employer.