The influence of mutation, selection and reproductive systems on within-population size variation at microsatellite loci was analysed using simulations. Mutation occurred through either (biased or unbiased) replication slippage, or unequal recombination between homologous chromosomes. Selection acted either on large allele size, or on the difference in size between the two homologous alleles of an individual. Reproduction was either sexual (panmictic) or clonal. Classical population genetics parameters, such as gene diversity or variance of allele size, were followed over (generally) 5000 generations for various sets of values of the mutation rate and strength of selection, in either clonally or sexually reproducing populations. The reproduction system had little influence on genetic parameters, either under neutral conditions or when selection acted on large allele size. Selection against difference in allele size strongly constrained variability in panmictic populations, whereas a limited influence was observed in clonal populations. Selection against the difference in allele size between the two alleles of an individual is an alternative explanation for the long life expectancy of microsatellite loci in sexual species. Whether this selection process actually occurs can therefore be tested by comparing the allele size distribution of microsatellite loci between regions/genomes exhibiting markedly different recombination rates.