Helical Tomotherapy (HT) has become increasingly popular over the past few years. However, its clinical efficacy and effectiveness continues to be investigated. Pre-treatment patient repositioning in highly conformal image-guided radiation therapy modalities is a prerequisite for reducing setup uncertainties. A MVCT image set has to be acquired to account for daily changes in the patient's internal anatomy and setup position. Furthermore, a comparison should be performed to the kVCT study used for dosimetric planning, by a registration process which results in repositioning the patient according to specific transitional and rotational shifts. Different image registration techniques may lead to different repositioning of the patient and, as a result, to varying delivered doses. This study aims to investigate the expected effect of patient setup correction using the Hi-Art tomotherapy system by employing radiobiological measures such as the biologically effective uniform dose (BEUD) and the complication-free tumor control probability (P+). In this study, a typical case of lung cancer with metastatic head & neck disease was investigated by developing a Helical Tomotherapy plan. For the Tomotherapy HiArt plan, the dedicated Tomotherapy treatment planning station was used. Three dose distributions (planned and delivered with and without patient setup correction) were compared based on radiobiological measures by using the P+ index and the BEUD concept as the common prescription point of the plans and plotting the tissue response probabilities against the mean target dose for a range of prescription doses. The applied plan evaluation method shows that in this cancer case the planned and delivered dose distributions with and without patient setup correction give a P+ of 81.6%, 80.9% and 72.2%, for a BEUD to the planning target volume (PTV) of 78.0Gy, 77.7Gy and 75.4Gy, respectively. The corresponding tumor control probabilities are 86.3%, 85.1% and 75.1%, whereas the total complication probabilities are 4.64%, 4.20% and 2.89%, respectively. HT can encompass the often large PTV required while minimizing the volume of the organs at risk receiving high dose. However, the effectiveness of a HT treatment plan can be considerably deteriorated if an accurate patient setup system is not available. Taking into account the dose-response relations of the irradiated tumors and normal tissues, a radiobiological treatment plan evaluation can be performed, which may provide a closer association of the delivered treatment with the clinical outcome. In such situations, for effective evaluation and comparison of different treatment plans, traditional dose based evaluation tools can be complemented by the use of P+,BEUD diagrams.