Background: Head and neck masses are common in infants, children and adolescents. Etiologically, these masses are divided into three groups of inflammatory, congenital and neoplastic lesions. Their incidence rate has been variable in different parts of the world. This study aimed to determine the frequency of head and neck masses in Iranian children during a 21-year period. Methods: This retrospective, descriptive study was performed on medical files of patients between 2 to 12 years with pathological head and neck masses derived from the archives of the Pathology Department of Children’s Medical Center of Tehran from 1995 to 2016. Age, gender, time of presentation, location of the lesions and final diagnosis were collected from patients' medical records and descriptively analyzed. Results: Of 594 children, 63.3% were males and 36.7% were females (male to female ratio of 1.7:1, P < 0.001). The mean age was 6.5 years (range 2 years and 2 months to 12 years). The highest prevalence belonged to inflammatory/reactive/infectious lesions (41.7%) followed by neoplastic lesions (35.7%) and congenital/developmental lesions (22.6%). In the neoplastic group, malignant and benign lesions had 26.6% and 9.1% prevalence, respectively. Lymphoma (22.4%; 16.3% Hodgkin and 6.1% non-Hodgkin), lymphadenitis (16.2%) and thyroglossal cyst (11%) were the most prevalent lesions. Conclusions: Based on the results, inflammatory lesions had the highest incidence among the head and neck masses in children. Malignant lesions were not uncommon among Iranian children.