The aim of this retrospective study was to evaluate the prognostic significance of paratracheal lymph node dissection including hemithyroidectomy for the development of hypo(para)thyroidism. From 1990 to 2004, 169 patients with a carcinoma of the larynx or hypopharynx who underwent paratracheal lymph node dissection were selected. Data of 137 patients (23 women, 114 men) were analyzed. Hundred patients were tested on thyroid function. Patient, tumor and treatment characteristics were noted including age, gender, site, TNM stage and details of surgery, radiotherapy and chemotherapy. Seventy percent of the tested patients had hypothyroidism (36% clinical, 34% subclinical); 33% had hypoparathyroidism. All patients with hypo(para)thyroidism underwent various lymph node treatment modalities. For the various treatment combinations, no increase of hypo(para)thyroidism was found if a bilateral paratracheal lymph node dissection was performed. The incidence of hypo(para)thyroidism after laryngectomy in combination with hemithyroidectomy, neck dissection and paratracheal lymph node dissection is high. An additional risk of paratracheal dissection for the development of hypo(para)thyroidism could not be shown.