Objectives To compare the three-dimensional (3D)-fast spinecho (FSE)-Cube with a conventional imaging protocol in evaluation of dacryostenosis. Methods Thirty-three patients with epiphora underwent examinations using Cube magnetic resonance dacryocystography (MRD) and a conventional protocol, which included 3D fast-recovery fast spin-echo (FRFSE) MRD and two-dimensional (2D)-FSE sequences at 3.0 T. Using lachrymal endoscopic findings as the reference standard, we calculated the sensitivity and specificity of both protocols for detecting lachrymal drainage system (LDS) obstruction and their accuracies in depicting the level of obstruction. Comparable coronal and axial images were selected for bot sequences. Two neuroradiologists graded paired images for blurring, artefacts, anatomic details, and overall image quality. Results The two methods showed no significant difference in sensitivity (89.5 % vs. 94.7 %; p = 0.674), specificity (64.3 %; p = 1) or accuracy (86.8 %; p = 1) in detecting or depicting LDS obstruction. Blurring and artefacts were significantly better on 2D-FSE images (p < 0.01 and p < 0.05, respectively). Anatomic details were significantly better on Cube reformats (p < 0.001). No significant difference existed in overall image quality (p > 0.05). Conclusions In comparison with the conventional protocol, Cube MRD demonstrates satisfactory image quality and similar diagnostic capability for cases of possible LDS disease.