MetaQTL is a suite of programs designed to carry out meta-analysis of QTL mapping experiments. A QTL mapping experiment consists in a genetic linkage map and a set of quantitative trait loci (QTL) which have been detected and positioned onto the genetic linkage map. This package is composed by several programs written in pure Java. This programs can perform various tasks, including reformatting, analyzing data and visualizing the results of the analyses. Presently the programs can handle data from backcross, intercrosses and recombinant inbreds, as well as a few other experimental designs. This project is ongoing and suggestions are welcome for further improvments and enhancements.