In order to analyze the magnitude of set up errors corrected by Helical TomoTherapy Mega-Voltage CT on a daily or weekly basis and their impact on the delivered dose to the tumor and organs at risk (OAR), the setup errors of 6 nasal cavity and 4 nasopharyngeal cancer patients who were treated with Helical Tomotherapy for 25-33 fractions were retrospectively analyzed. Each patient had MVCT guided repositioning for all fractions of treatment. The new dose volume histogram (DVH) and equivalent uniform dose (EUD) for planning target volume (PTV) and OARs were calculated for hypothetical situations where no imaging guidance (IG) or once weekly image guidance (WIG) took place. The mean total set up error if treated without daily IG was 3.6+/-1.0 mm, which can be reduced to 1.7+/-0.6 mm if a WIG was performed. The geometrical uncertainties from the absence of image guidance resulted in a reduction of mean PTV EUD dose by 2.1+/-1.0 %, which can be reduced to 1.4+/-1.0 % with WIG. The EUD of OARs increased 1.8+/-2.0 Gy or 0.8+/-1.3 Gy without or with WIG respectively. Without daily IG, the mean patient position uncertainty has relatively small impacts on the mean PTV and OAR dosimetry, which can be further reduced approximately by half using a WIG. On the other hand, because of the large variance, with low probability, substantial deviation from the original planned dosimetry may occur without IG. Therefore, daily MVCT is preferred as an important safety measure in the IMRT.