Objective To evaluate the value of MSCT in differentiate cystic lesions in different cervical region. Methods Forty cases with cyst lesions in the neck which was confirmed by pathology were collected in our study. The following diseases were excluded: cystic lesions from thyroid gland and thymus or bronchus, cystic changes of solid lesions ( necrotic lymph node) and cystic or solid lesions in the parotid gland. All patients underwent MSCT scan on GE Lightspeed 16. The parameters were following: 120 kV,260 mA, thickness 5 mm, pitch 1. 375. The delay time for contrast enhanced CT was 25 seconds for arterial phase and 60 seconds for vein phase. Results Lesions were analyzed in 4 different cervical regions including parotid gland, midline, lateral cervix and posterior cervix. Among the lesions in parotid area,2 were first brachial cyst and the other 2 were epidermoid cyst. First brachial cyst occurred intraparotid gland and epidermoid cyst occurred intraparotid or extraparotid gland. Among the lesions in midline area, 17 cases were thyroglossal cysts,81.0% were in the level hyoid bone, 12 cases of thyroglossal cysts protruded at the preepiglottic space or oral base. Another kind of lesions in midline included 3 cases of epiglottic cysts and 1 epidermoid cyst in the lower level of the neck which involved infrasternal level. The 12 cases of second brachial cysts occurred in the lateral neck. Ten cases were in the left side. Type Ⅱ was the most common type and account for 5 cases among all of second brachial cysts. Type Ⅰ and type Ⅱ were running up,accounting 3 cases respectively. Type Ⅳ account for 1 case. Two cases with lymphangioma and 1 case with third brachial cyst located at the posterior neck. Conclusion According to the location and typical imaging appearance, MSCT can do the differentiation of different cystic lesions in the different area of neck.