Quantitative trait loci (QTL) mapping tools such as MapQTL and R/qtl allow easy and fast analysis of more than one trait at the same time. However, for experiments with large datasets, such as high-throughput metabolite QTL analysis, these tools do not provide an easy-to-inspect summary of the results. The ability to have an overview of the distribution of the identified QTL becomes a key factor. MQ2 fills this need by providing a command line tool and a web application that summarizes and visualizes the results of multi-trait QTL analysis. MQ2 can use the output of commonly used QTL analysis tools, such as MapQTL and R/qtl, as input. MQ2 can be used for free at: http://www.plantbreeding.wur.nl/mq2/.