Understanding the forces that govern the distribution of single nucleotide polymorphisms is vital for many of their applications. Here we conducted a systematic search to quantify how both SNP density and human-chimpanzee divergence vary around different repetitive sequences. We uncovered a highly complicated picture in which these quantities often differ significantly from the genome-wide average in regions extending more than 20 kb, the direction of the deviation varying with repeat number and motif. AT microsatellites in particular are potent predictors of SNP density, long (AT)(n) repeat tracts tending to be found in regions of significantly reduced SNP density and low GC content. Although the causal relationships remain difficult to determine, our results indicate a strong relationship between microsatellites and the DNA that flanks them. Our results help to explain the mixed picture that emerges from other studies and have important implications for the way in which genetic diversity is distributed in our genomes.