The equilibrium level of inbreeding depression in populations with different selfing rates is studied for models with symmetrical or asymmetrical heterozygous advantage at several loci with partial linkage. As for the case of a single locus, the inbreeding depression caused by loci with heterozygous advantage can be higher for partially selfing populations than for complete outcrossing. The spread of modifier alleles at another locus that affects the selfing rate is studied. The stability of outcrossing populations to invasion by alleles that give increased selfing is found to depend on levels of inbreeding depression being greater than one-half, in accordance with earlier models that assumed a fixed level of inbreeding depression. However, in partially selfing populations the spread of such alleles can be checked by smaller levels of inbreeding depression than one-half, so that they do not always spread to fixation. This is interpreted as being due to associations between the genotypes at the modifier locus and the selected loci, together with increasing inbreeding depression as selfing increases, and does not occur if the inbreeding depression is due to mutation-selection balance.