The aim of this study was to evaluate the impact of actual rotational setup errors on dose distributions in intracranial stereotactic radiotherapy (SRT) with different alternatives for treatment position selection. A total of 38 SRT fractions from 18patients were retrospectively evaluated with rotational setup errors obtained from actual treatments. The planning computed tomography (CT) images were rotated according to online cone-beam CT (CBCT) images and the dose distribution was recalculated to the rotated CT images using three different patient positionings derived from: 1) an automatic 6D match neglecting rotation correction (Auto6D); 2) an automatic 3D match (Auto3D); and 3) a manual 3D match from actual treatment (Treat3D). The mean conformity index (CI) was 0.92 for the original plans and 0.91 for the Auto6D plans. The mean CI decreased significantly (p < 0.01) to 0.78 and 0.80 for the Auto3D and the Treat3D plans, respectively. The mean minimum dose of the planning target volume (PTVmin) was 91.9% of the prescribed dose for the original plans and 92.1% for the Auto6D plans, while for the Auto3D and the Treat3D plans PTVmin decreased significantly (p < 0.01) to 78.9% and 80.2%, respectively. No significant differences were seen between the Auto6D and the original treatment plans in terms of the dose parameters. However, the Auto3D and the Treat3D plans were statistically significantly inferior (p < 0.01) to the Auto6D and the original plans. In addition, a significant negative correlation (p < 0.01, |r| > 0.38) was found in the Auto3D and the Treat3D cases between the rotation error and CI, PTVmin or minimum dose of gross tumour volume. In SRT, a treatment plan of comparable quality to 6D rotation correction can be achieved by using 6D registration without a rotational correction in the selection of patient positioning. This was demonstrated for typical rotation errors seen in clinical practice.