Previous studies of mitochondrial DNA (mtDNA) in Europe and the Near East have suggested that, in contrast with classical markers and the Y chromosome, mtDNA does not exhibit significant geographical structuring. Here, we show that, with a sufficiently large sample size and a better resolved mtDNA tree, clades of mtDNA do indeed exhibit gradients similar to those of other marker systems. However, the more detailed analyses afforded by molecular sequence data suggest that the explanations for these gradients are likely to be much more complex than those proposed for classical markers.