This study quantifies the dose prediction errors (DPEs) in dynamic IMRT dose calculations resulting from (a) use of an intensity matrix to estimate the multi-leaf collimator (MLC) modulated photon fluence (DPEIGfluence) instead of an explicit MLC particle transport, and (b) handling of tissue heterogeneities (DPEhetero) by superposition/convolution (SC) and pencil beam (PB) dose calculation algorithms. Monte Carlo (MC) computed doses are used as reference standards. Eighteen head-and-neck dynamic MLC IMRT treatment plans are investigated. DPEs are evaluated via comparing the dose received by 98% of the GTV (GTV D-98%), the CTV D-95%, the nodal D-90%, the cord and the brainstem D-02%, the parotid D-50%, the parotid mean dose (D-Mean), and generalized equivalent uniform doses (gEUDs) for the above structures. For the MC-generated intensity grids, DPEIGfluence is within 2.1% for all targets and critical structures. The SC algorithm DPEhetero is within 3% for 98.3% of the indices tallied, and within +/- 3.4% for all of the tallied indices. The PB algorithm DPEhetero is within 3% for 92% of the tallied indices. Statistical equivalence tests indicate that PB DPEhetero requires a 3.6% interval to state equivalence with the MC standard, while the intervals are < 1.5% for SC DPEhetero and DPEIGfluence. Overall, these results indicate that SC and MC IMRT dose calculations which use MC-derived intensity matrices for fluence prediction do not introduce significant dose errors compared with full Monte Carlo dose computations; however, PB algorithms may result in clinically significant dose deviations. (c) 2007 American Association of Physicists in Medicine.