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Summary Objective Thyroglossal duct (TD) anomalies are generally considered to be a distinct clinical entity. However occasional cases do not conform to the standard picture and are complex. This study aimed to scrutinise consecutive cases of TD anomaly managed surgically over 7 years at a tertiary teaching hospital and analyse those with atypical features. Methods This is a retrospective study of 62 children managed for a clinical diagnosis of TD anomaly from 1998 to 2005. Their medical records were reviewed for clinical presentation, investigations, operative findings, histopathology, management and outcome. After a clinical diagnosis, they had individualized investigations (USG, MRI, radioiodine scan, FNA) prior to the Sistrunk operation. Results 5/62 cases had atypical features. 2/5 were adolescents with a short history while 3 were below 5 years of age with onset since infancy. 4/5 were females. 1/5 had a Sistrunk operation earlier, 2/5 had a redo surgery prior to cure. 3/5 had a grossly identifiable tract at surgery, one with a midline course and two deviating laterally to open at the left pharyngeal wall. The final histological diagnosis was a mixed thyroglossal-dermoid cyst (case 1), TD anomalies with aberrant pharyngeal communication (cases 2 and 3), isthmic thyroglossal ‘cold’ cyst (case 4), and a tuberculous cyst (case 5). Postoperatively, Cases 2 and 3 had wound infections that were managed conservatively while case 5 developed an incisional sinus that healed after a month of anti-tuberculous chemotherapy. Cases 1 and 4 had an uneventful recovery. At an average f/u of 2 years, all are asymptomatic and well. Conclusions 5–10% of apparent TD anomalies may present with atypical clinicopathologic characteristics. Atypical cases and late presentations may warrant additional investigations to establish the diagnosis and tailor management.