Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations enabled the investigation of the genetic architecture of gene expression variation. This has the potential to enrich the understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. For Arabidopsis thaliana a number of genetical genomics studies have been published, uncovering many expression quantitative trait loci (eQTLs). Yet, this complex data is not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this with AraQTL www.bioinformatics.nl/AraQTL/, an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local-eQTLs that could harbour candidate genes for phenotypic QTL, or detect gene-by-environment interactions by comparing eQTLs under different conditions.