Our aim was to compare the perfusion [blood flow (BF)] values obtained by first-pass dynamic contrast-enhanced (DCE) T2-weighted magnetic resonance (MR) and computed tomography (CT) imaging of squamous cell carcinoma (SCC) in the upper aerodigestive tract in the same patient population. Seventeen patients with histologically proven primary SCC of the upper aerodigestive tract were prospectively evaluated. The perfusion CT studies were obtained using a 16-row multi-slice CT scanner running a commercial software package with a deconvolution-based technique; while the perfusion MR studies (1.5 T) were analysed with in-house-written MR perfusion software based also on a deconvolution technique. The mean perfusion values of SCC assessed by perfusion CT and MR imaging were 68.93 +/- 31.61 and 81.56 +/- 49.25 ml/min/100 g, respectively. The Bland-Altman graph showed a proportional error in the perfusion values measured by DCE-CT and -MR imaging; however, the degree of agreement was acceptable (95% limits of agreement: -66.1 to 40.8). Regression analysis of the perfusion values demonstrated significant correlation between the modalities: BF(MR) = 1.34 x BF(CT) - 10.93 (P < 0.0005, r (2) = 0.74). The parametric maps generated by both modalities provided insights into the tumour perfusion, while analysis of the obtained perfusion values demonstrated that both modalities may be used interchangeably in SCC in the upper aerodigestive tract.