Objectives Both benign tumors and cysts in the oral and maxillofacial region show clear borders and homogeneously high signal intensity on magnetic resonance (MR T2-weighted images, making differentiation difficult without contrast enhancement. Windowing for brightness and contrast adjustment may be helpful in interpreting relative signal intensities on MR images. This study was performed to determine whether re-windowing against targeted lesions on T2-weighted images was a useful procedure that would enhance differentiation without invasive contrast enhancement. Methods Twenty-six lesions (13 benign tumors, 13 cysts) that showed clear borders and homogeneously high signal intensity on T2-weighted images were examined. The windowing parameters of axial images were readjusted to emphasize contrast only inside the lesions using automatic density adjustment. Re-windowed images were reviewed by three experienced oral radiologists and categorized based on the internal homogeneity of the lesion into four grades: 0, heterogeneous; 1, slightly heterogeneous; 2, slightly homogeneous; 3, homogeneous. Re-windowing was then evaluated for its usefulness in differentiating between benign tumors and cysts. Results For cysts, the rates of homogeneous (grades 3 and 2) and heterogeneous intensity (grades 1 and 0) were 66.7 (26/39) and 33.3% (13/39), respectively. For benign tumors, these rates were 33.3 (13/39) and 66.7% (26/39), respectively. Cysts showed a higher rate of homogeneous intensity, while the opposite was true for benign tumors. A significant difference in distribution was observed between cysts and benign tumors (P \ 0.01, v 2 test). Conclusion Re-windowing for T2-weighted images is helpful in differentiating between benign tumors and cysts with clear borders and homogeneously high signal intensity on T2-weighted images.