We present a case report of a small boy with cystic fibrosis complicated by pertussis and pneumothorax. The child had not been vaccinated against Bordetella pertussis due to the failure to thrive and was infected with the bacterium at the age of 4 months. The course of the disease was severe, with respiratory distress and spontaneous pneumothorax. The diagnosis of pertussis was serologically confirmed. A suspicion for cystic fibrosis increased after an unusually prolonged course of the disease and a history of the failure to thrive. A comprehensive diagnostic procedure revealed Pseudomonas aeruginosa respiratory infection, anemia, pancreatic insufficiency, a positive sweat test and the presence of two CFTR gene mutations. The patient, treated with comprehensive cystic fibrosis therapy, recovered from acute respiratory illness and started to thrive soon.