We used computer simulations to investigate to what extent true inbreeding, i.e. identity-by-descent, is affected by the use of marker-assisted selection (MAS) relative to traditional best linear unbiased predictions (BLUP) selection. The effect was studied by varying the heritability (h(2) = 0.04 vs. 0.25), the marker distance (MAS vs. selection on the gene, GAS), the favourable QTL allele effect (alpha = 0.118 vs. 0.236) and the initial frequency of the favourable QTL allele (p = 0.01 vs. 0.1) in a population resembling the breeding nucleus of a dairy cattle population. The simulated genome consisted of two chromosomes of 100 cM each in addition to a polygenic component. On chromosome 1, a biallelic QTL as well as 4 markers were simulated in linkage disequilibrium. Chromosome 2 was selectively neutral. The results showed that, while reducing pedigree estimated inbreeding, MAS and GAS did not always reduce true inbreeding at the QTL relative to BLUP. MAS and GAS differs from BLUP by increasing the weight on Mendelian sampling terms and thereby lowering inbreeding, while increasing the fixation rate of the favourable QTL allele and thereby increasing inbreeding. The total outcome in terms of inbreeding at the QTL depends on the balance between these two effects. In addition, as a result of hitchhiking, MAS results in extra inbreeding in the region surrounding QTL, which could affect the overall genomic inbreeding.