Our aim in this study was to examine the power of associative overdominance in creating a correlation between individual heterozygosity and fitness and in maintaining genetic polymorphism at neutral loci. This was undertaken by simulating a diploid model with five chromosomes, each with 1000 loci that could have deleterious mutations linked to neutral markers located on the same chromosomes. The simulations were carried out with various combinations of the following parameters: population size (N), number of crossovers (c), selection coefficient (s) and dominance (h). All combinations of parameter values resulted in a positive regression of the fitness on the individual marker heterozygosity, although the fitness differences were not very large when c = 2. The association between individual heterozygosity and fitness was clearest for recessive mutations (small h) with intermediate selection coefficients in small populations. The level of marker heterozygosity in the population was higher than the neutral expectation for many parameter values, even though regression of fitness on heterozygosity was not always steep at the individual level. These results agreed with the conclusion that associative overdominance could help to maintain polymorphisms in small populations. Strong selection occasionally yielded gene diversities lower than the neutral expectation, reflecting the prediction that strong selection reduces the effective population size.