Abstract Summary: Commonly used multiplicity adjustments fail to control the error rate for reported findings in many expression quantitative trait loci (eQTL) studies. TreeQTL implements a hierarchical multiple testing procedure which allows control of appropriate error rates defined relative to a grouping of the eQTL hypotheses. Availability and Implementation: The R package TreeQTL is available for download at http://bioinformatics.org/treeqtl. Contact: sabatti@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.