The aim of this study was to identify clinical factors that can predict malignancy in patients with persistent cervical lymphadenopathy. This retrospective study included 575 patients with persistent cervical lymphadenopathy who underwent surgical excision. The patients were divided into two groups according to their ages: group 1 (≤18 years) and group 2 (>18 years). Multiple logistic regression models and univariate analysis were performed to determine the association between clinical factors and malignancy. Male gender [odds ratio (OR) 4.184, 95 % confidence interval (CI) 1.823-9.602, p = 0.001], increased age (OR 1.072, 95 % CI 1.001-1.148, p = 0.046), left-sided lesions (OR 3.423, 95 % CI 1.407-8.329, p = 0.007), and larger lymph node size (OR 1.445, 95 % CI 1.021-2.044, p = 0.038) were significantly associated with malignancy in group 1. Male gender (OR 3.761, 95 % CI 2.361-5.992, p = 0.001), increased age (OR 1.015, 95 % CI 1.003-1.027, p = 0.018), duration of the disease (OR 0.770, 95 % CI 0.668-0.888, p = 0.001), and the presence of B symptoms (OR 4.996, 95 % CI 2.862-8.721, p = 0.001) were significantly associated with malignancy in group 2. The sensitivity and specificity of the models were 84 and 61.5 % for group 1 and 77.9 and 67.9 % for group 2, respectively. Increasing age and male gender were found to be associated with malignancy in all age groups. Larger lymph node size and left-sided lymphadenopathy were significant predictors of malignancy in children. Presence of B symptoms was found to be associated with malignancy in adults. Our results indicated that increasing duration of lymphadenopathy and the presence of bilaterality render the lymph node more likely to be benign in adults. No significant association was found between the involved neck site and malignancy for all age groups.