The effects of factors known to influence the level of polymorphism at microsatellite loci were studied using 99 markers and seven lines of bread wheat. Mutational factors as well as indirect selective events shape diversity at these loci. Theory predicts that the selection of favorable alleles should reduce polymorphism at neutral neighboring loci in genomic areas with low recombination rates. In wheat, local recombination rate is positively correlated with physical distance from the centromere. Seventy four loci among the 99 used could be physically located on the chromosome. We studied how the following affected the diversity among a set of inbred lines: the length of the alleles, the motif (CA versus CT), the structure of the loci (perfect versus imperfect) and the chromosomal position of the loci. For each locus, we determined whether the polymorphism observed at a locus was compatible with the Stepwise Mutation Model (SMM) or the Two-Phase Model (TPM). Both the mutation rate and the compatibility with the SMM or the TPM were shown to be variable between loci. Wheat microsatellite loci were found to be more variable when segregating alleles were perfect and had long motifs (composed of many repetitions). Diversity observed at 19 loci was not compatible with the SMM. Loci located in distal regions, with presumably high recombination rates, had longer allele sizes and were more polymorphic than loci located in proximal regions. We conclude that both mutation factors and indirect selective events vary according to the local recombination rate and therefore jointly influence the level of polymorphism at microsatellite loci in wheat.