The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) by interval mapping was investigated using simulation. Confidence intervals were created using a non-parametric (resampling method) and parametric (resimulation method) bootstrap for a backcross population derived from inbred lines. QTLs explaining 1%, 5% and 10% of the phenotypic variance were tested in populations of 200 or 500 individuals. Results from the two methods were compared at all locations along one half of the chromosome. The non-parametric bootstrap produced results close to expectation at all non-marker locations, but confidence intervals when the QTL was located at the marker were conservative. The parametric method performed poorly; results varied from conservative confidence intervals at the location of the marker, to anti-conservative intervals midway between markers. The results were shown to be influenced by a bias in the mapping procedure and by the accumulation of type 1 errors at the location of the markers. The parametric bootstrap is not a suitable method for constructing confidence intervals in QTL mapping. The confidence intervals from the non-parametric bootstrap are accurate and suitable for practical use.