BACKGROUND: Although malignancy has been reported in thyroglossal cysts, synchronous occurrence of two malignancies is extremely rare. CASE REPORT: A case of concurrent papillary and squamous carcinoma arising in the thyroglossal cyst is presented here. CONCLUSIONS: Papillary and squamous carcinoma simultaneously occurring in a thyroglossal cyst is rarely diagnosed prior to surgery and pose a therapeutic dilemma. In view of the extreme rarity of the condition, controversies do exist regarding the optimal strategy to be adopted. The ideal procedure needs to be individually tailored and involve a combination of surgery, radio ablation, thyroid suppression and external radiotherapy.