Differences in recombination rates along the chromosomes can influence the evolution of neutral loci via hitchhiking effects. Generally, these effects should be stronger in regions of low recombination than in regions of high recombination. Detailed information on physical and genetic maps in the house mouse now allows an assessment of the correlation between neutral variability and recombination rates at given chromosomal regions. We chose 29 microsatellite loci from chromosomal regions which show differences in recombination rates and tested their variability in samples from five wild populations of Mus musculus musculus and M. m. domesticus. Our results provide no evidence for a correlation between microsatellite variability and recombination rates. This suggests that the high average mutation rate of microsatellites in mammals counterbalances the effects of long-range hitchhiking in the mouse genome. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 629–635.