Background: Both patient-specific dose recalculation and gamma passing rate analysis are important for the quality assurance (QA) of intensity modulated radiotherapy (IMRT) plans. The aim of this study was to analyse the correlation between the gamma passing rates and the volumes of air cavities (V-air) and bony structures (V-bone) in target volume of head and neck cancer. Methods: Twenty nasopharyngeal carcinoma and twenty nasal natural killer T-cell lymphoma patients were enrolled in this study. Nine-field sliding window IMRT plans were produced and the dose distributions were calculated by anisotropic analytical algorithm (AAA), Acuros XB algorithm (AXB) and SciMoCa based on the Monte Carlo (MC) technique. The dose distributions and gamma passing rates of the targets, organs at risk, air cavities and bony structures were compared among the different algorithms. Results: They values obtained with AAA and AXB were 95.6 +/- 1.9% and 96.2 +/- 1.7%, respectively, with 3%/2 mm criteria (p > 0.05). There were significant differences (p < 0.05) in the gamma values between AAA and AXB in the air cavities (86.6 +/- 9.4% vs. 98.0 +/- 1.7%) and bony structures (82.7 +/- 13.5% vs. 99.0 +/- 1.7%). Using AAA, they values were proportional to the natural logarithm of V-air (R-2 = 0.674) and inversely proportional to the natural logarithm of V-bone (R-2 =0.816). When the V-air, in the targets was smaller than approximately 80 cc or the V-bone in the targets was larger than approximately 6 cc, the gamma values of AAA were below 95%. Using AXB, no significant relationship was found between the gamma values and V-air or V-bone. Conclusion: In clinical head and neck IMRT QA, greater attention should be paid to the effect of V-air and V-bone in the targets on they passing rates when using different dose calculation algorithms.