Background Dysphagia is a common consequence of treatment for head and neck cancer (HNC). The purpose of the study was to evaluate the prevalence of dysphagia in a group of patients treated for HNC in Slovenia, and to identify factors contributing to the development of dysphagia. Patients and methods One-hundred-nine consecutive patients treated for HNC at two tertiary centers were recruited during their follow-up visits. They fulfilled EORTC QLQ-H&N35 and "Swallowing Disorders after Head and Neck Cancer Treatment questionnaire" questionnaires. Patients with dysphagia were compared to those without it. Results Problems with swallowing were identified in 41.3% of the patients. Dysphagia affected their social life (in 75.6%), especially eating in public (in 80%). Dysphagia was found the most often in the patients with oral cavity and/or oropharyngeal cancer (in 57.6%) and in those treated less than 2 years ago (p = 0.014). In univariate analysis, a significant relationship was observed between dysphagia prevalence and some of the consequences of anti-cancer treatment (impaired mouth opening, sticky saliva, loss of smell, impaired taste, oral and throat pain, persistent cough, and hoarseness), radiotherapy (p = 0.003), and symptoms of gastroesophageal reflux (p = 0.027). After multiple regression modelling only persistent cough remained. Conclusions In order to improve swallowing abilities and, consequently, quality of life of the patients with HNC a systematic rehabilitation of swallowing should be organized. A special emphasis should be given to gastroesophageal reflux treatment before, during and after therapy for HNC.