The NIDDK Genomics Core Facility provides next-generation sequencing (NGS) service on a cost-recovery basis to the NIH intramural community, with priority for NIDDK users. Additional resources in support of this technology included consultation services, user-accessible instrumentation, bioinformatics infrastructure, and secure data management. NGS data generated by the facility are used to study diseases of programmatic interest, such as diabetes, metabolic disorders, and liver and gastrointestinal diseases. Applications of the technology include the analysis of gene expression, the determination of targets for DNA and RNA-binding proteins, the identification of mutations relevant to disease, and the characterization of epigenetic chromatin modification. The facility offers high-throughput, next-generation sequencing on the Illumina platform. Users are responsible for sample preparation. Support from Core staff includes assistance with experimental design and guidance on library construction. The facility houses a shared instrumentation laboratory and provides training for users. Instruments are available for sample shearing, automated chromatin immunoprecipitation, automated library construction, library quality assessment and purification, and real-time qPCR. Users provide libraries to the facility, and submit library information via the sample tracking website. Core personnel assess library quality, perform sequencing, assess data quality, and perform alignment. Data is returned to users by secure FTP. Users are responsible for additional analysis. The Core provides access to integrated software packages for NGS data analysis. As time permits, additional bioinformatics support from Core personnel may be available on an ad hoc, collaborative basis.