The purpose of this study was to identify the spectrum of cytological diagnoses and evaluate the diagnostic effectiveness of fine needle aspiration cytology (FNA) in patients less than 20 years old. The subjects were selected by retrospectively reviewing records from 1999 to 2009. Selected patients less than 20 years old underwent FNA. Cytological and histological slides of samples from the subjects were reviewed. Our study included a total of 909 subjects with a mean age of 14.6 years. The majority of the FNA samples were taken from lymph nodes (n = 448, 49.3%), with the remaining aspirates obtained from the thyroid gland (n = 247, 27.2%), soft tissues of head and neck masses (n = 106, 11.7%), salivary glands (n = 75, 8.3%), breasts (n = 18, 1.9%), skins (n = 9, 1.0%) and soft tissues of extremity (n = 6, 0.7%). The majority (87.6%, n = 796) of the FNA samples were categorized as 'benign', with the remaining designated as 'atypical lesion' (n = 18, 2.0%), 'malignant' (n = 24, 2.6%), or 'inadequate specimen' (n = 71, 7.8%). FNA accuracy was 92% for diagnosing cancer. Specificity and sensitivity were 99% and 63%, respectively. Our study first revealed that FNA has a high specificity for diagnosing cancer in various anatomical locations in young patients and can be confidently used as an effective tool for diagnosing malignancies in young individuals with a clinically suspicious lesion.