To date, most intensity-modulated radiation therapy (IMRT) delivery has occurred using linear accelerators (linacs), although helical tomotherapy has become commercially available. To quantify the dosimetric difference, we compared linac-based and helical tomotherapy-based treatment plans for IMRT of the oropharynx. We compared the dosimetry findings of 10 patients who had oropharyngeal carcinoma. Five patients each had cancers in the base of the tongue and tonsil. Each plan was independently optimized using either the CORVUS planning system (Nomos Corporation, Sewickly, PA), commissioned for a Varian 2300 CD linear accelerator (Varian Medical Systems, Palo Alto, CA) with 1-cm multileaf collimator leaves, or helical tomotherapy. The resulting treatment plans were evaluated by comparing the dose-volume histograms, equivalent uniform dose (EUD), dose uniformity, and normal tissue complication probabilities. Helical tomotherapy plans showed improvement of critical structure avoidance and target dose uniformity for all patients. The average equivalent uniform dose reduction for organs at risk (OARs) surrounding the base of tongue and the tonsil were 17.4% and 27.14% respectively. An 80% reduction in normal tissue complication probabilities for the parotid glands was observed in the tomotherapy plans relative to the linac-based plans. The standard deviation of the planning target volume dose was reduced by 71%. In our clinic, we use the combined dose-volume histograms for each class of plans as a reference goal for helical tomotherapy treatment planning optimization. Helical tomotherapy provides improved dose homogeneity and normal structure dose compared with linac-based IMRT in the treatment of oropharyngeal carcinoma resulting in a reduced risk for complications from focal hotspots within the planning target volume and for the adjacent parotid glands.