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Abstract Background To assess the utility of histogram and texture analysis of magnetic resonance (MR) fat-suppressed T2-weighted imaging (Fs-T2WI) for the prediction of histological diagnosis of head and neck squamous cell carcinoma (SCC) and malignant lymphoma (ML). Methods The cases of 57 patients with SCC (45 well/moderately and 12 poorly differentiated SCC) and 10 patients with ML were retrospectively analyzed. Quantitative parameters with histogram features (relative mean signal, coefficient of variation, kurtosis and skewness) and gray-level co-occurrence matrix (GLCM) features (contrast, correlation, energy and homogeneity) were calculated using Fs-T2WI data with a manual tumor region of interest (ROI). Results The following significantly different values were obtained for the total SCC versus ML groups: relative mean signal (3.65 ± 0.86 vs. 2.61 ± 0.49), contrast (72.9 ± 16.2 vs. 49.3 ± 8.7) and homogeneity (2.22 ± 0.25 × 10− 1 vs. 2.53 ± 0.12 × 10− 1). In the comparison of the SCC histological grades, the relative mean signal and contrast were significantly lower in the poorly differentiated SCC (2.89 ± 0.63, 56.2 ± 12.9) compared to the well/moderately SCC (3.85 ± 0.81, 77.5 ± 13.9). The homogeneity in poorly differentiated SCC (2.56 ± 0.15 × 10− 1) was higher than that of the well/moderately SCC (2.1 ± 0.18 × 10− 1). Conclusions Parameters obtained by histogram and texture analysis of Fs-T2WI may be useful for noninvasive prediction of histological type and grade in head and neck malignancy.