Summary: We present a method to identify approximately independent blocks of linkage disequilibrium in the human genome. These blocks enable automated analysis of multiple genome-wide association studies. Availability and implementation: code: http://bitbucket.org/nygcresearch/ldetect; data: http://bitbucket.org/nygcresearch/ldetect-data. Contact: tberisa@nygenome.org Supplementary information: Supplementary data are available at Bioinformatics online.