BACKGROUND Detection rate of retropharyngeal lymph node metastasis in patients with nasopharyngeal carcinoma (NPC) needs to be improved. The purpose of this study was to compare three magnetic resonance (MR) sequences for detecting lymph nodes in patients with NPC. METHODS Between July 2007 and March 2008, MR staging of pre-treated tumor was conducted on 120 patients with pathologically confirmed NPC. The outcome of three different sequences for MR NPC staging were compared: coronal short TI inversion recovery (STIR), axial proton density fat-suppressed (PDWI fs), and coronal contrast enhanced fast spin echo T1 weighted fat-suppressed (CE FSE T1WI fs). Nodal classification method (1999) was applied to count the number of retropharyngeal and cervical lymph nodes discovered by each MR sequence. Paired t tests were used for statistical analysis. RESULTS A total of 2575 lymph nodes were found using coronal STIR sequence; 1816 lymph nodes for coronal CE FSE T1WI fs sequence and 2638 lymph nodes for axial PDWI fs sequence. Significant differences existed in the number of lymph nodes detected by axial PDWI fs and coronal CE FSE T1WI fs sequence (paired t test, P < 0.05), with the former sequence getting higher numbers. Statistical differences also existed between coronal STIR and coronal CE FSE T1WI fs sequence (paired t test, P < 0.05), with the former sequence getting higher numbers. No significant difference was found between coronal STIR sequence and axial PDWI fs sequence (paired t test, P > 0.05). CONCLUSIONS For the detection of retropharyngeal and cervical lymph nodes, coronal STIR sequence and axial PDWI fs sequence have similar performance and both sequences showed better detection than CE FSE T1WI fs sequence. Furthermore, by combining coronal STIR sequence and axial PDWI fs sequence, we can improve the detection of lymph nodes in NPC N-staging before treatment, especially for lymph nodes located in the thoracic entrance.