Background: To assess the risk factors for malignant lymph node (LN) in patients who had indeterminate fine-needle aspiration cytology of their cervical LNs. Methods: This was a retrospective study, where the neck ultrasound (US) and US-guided fine-needle aspiration were performed between July 2007 and August 2013. The patients who had indeterminate cytological reports were included. The age, sex, prior history of malignancy, side, short axis, long axis, short-axis to long-axis (S/L) ratio, and the ultrasonographic features including architecture, boundary, calcification, echogenicity, hilar echo, internal echo and vascular pattern were assessed. These characteristics were compared according to the final diagnoses either by pathological reports or clinical evaluations. Results: The final diagnoses showed that there were 40 benign and 19 malignant LNs in 59 patients who had indeterminate cytological reports. Comparing the characteristics between the final benign and malignant results by using multivariate analyses, there were three independent risk factors for predicting malignant LNs: long axis more than 1.75 cm (p = 0.03, odds ratio [OR] = 4.67 [1.14-19.1]), S/L ratio more than 0.6 (p = 0.02, OR = 10.84 [1.40-84.1]) and vague boundary (p < 0.01, OR = 12.33 [1.92-79.1]). Conclusions: The long axis more than 1.75 cm, S/L ratio more than 0.6 and vague boundary were the risk factors for predicting malignant LNs in patients who had indeterminate cytological reports of their cervical LNs.