WebQTL is an Internet facility for interactive analysis of complex phenotypes in recombinant inbred strains using quantitative trait locus detection and other genetic correlation approaches. The BXD recombinant inbred mice are a unique resource for genetic analysis because they are fully inbred and contain recombinant chromosomes of two sequenced progenitors, C57BL/6J and DBA/2J. Approximately 40 lines are usable today, and more are being developed. These lines can be maintained indefinitely, and data collected in them can be stored and reanalyzed in light of new technologies, unlike other mapping panels which can not be replicated. These mice have been studied extensively in over 20 years of existence. Genotypes at over 750 locations are known for these strains, over 600 behavioral, anatomical, physiological and other higher order phenotypes have been collected by a large number of investigators. Microarray measures of gene expression have been collected in the forebrain, cerebellum, hematopoietic stem cells and a growing number of other tissues. Sequence analysis has led to identification of single nucleotide polymorphisms in these strains, allowing large quantitative trait loci to be refined to small regions and often to a small handful of polymorphisms. Extensive links to external resources facilitate data interpretation. Multilevel data integration in WebQTL allows users a powerful new way to explore the effects of naturally occurring genetic variation on individual differences in gene expression and other higher order phenotypes.