In this work, a method for direct incorporation of patient motion into tomotherapy dose calculations is developed and validated. This computational method accounts for all treatment dynamics and can incorporate random as well as cyclical motion data. Hence, interplay effects between treatment dynamics and patient motion are taken into account during dose calculation. This allows for a realistic assessment of intra-fraction motion on the dose distribution. The specific approach entails modifying the position and velocity events in the tomotherapy delivery plan to accommodate any known motion. The computational method is verified through phantom and film measurements. Here, measured prostate motion and simulated respiratory motion tracks were incorporated in the dose calculation. The calculated motion-encoded dose profiles showed excellent agreement with the measurements. Gamma analysis using 3 mm and 3% tolerance criteria showed over 97% and 96% average of points passing for the prostate and breathing motion tracks, respectively. The profile and gamma analysis results validate the accuracy of this method for incorporating intra-fraction motion into the dose calculation engine for assessment of dosimetric effects on helical tomotherapy dose deliveries.