Helical tomotherapy presented many unique dosimetric challenges and solutions during the initial commissioning process, and some of them are presented. The dose calculation algorithm is convolution/superposition based. This requires that the energy fluence spectrum and magnitude be quantified. The methodology for doing so is described. Aspects of the energy fluence characterization that are unique to tomotherapy are highlighted. Many beam characteristics can be measured automatically by an included megavoltage computed tomography imaging system. This greatly improves data collection efficiency.