One-, two- and three-locus models of selection and mutation in completely self-fertilizing populations are examined. Equilibrium frequencies can be determined for these systems. Numerical analyses indicate that random genetic drift attributable to selfing plays a major role in determining equilibrium frequencies, even when strong directional selection is operating. Linkage has no effect on marginal gene frequencies or single-locus heterozygosity at equilibrium. The only model of those examined which leads to linkage disequilibrium is disruptive selection. In that model, selection reinforced the effect of selfing in favoring the homozygous genotypes.