The incidence of respiratory tract infections caused by Mycoplasma, Chlamydophila pneumoniae and Bordetella pertussis in children increases in the infectious season of autumn-winter-spring. Infection with atypical bacteria manifests with slightly increased body temperature, dry cough and headaches. However, these clinical signs are insufficient to determine the aetiology of individual atypical forms of pneumonia. The aim of the study was to outline the clinical picture of children with atypical and pertussis-related pneumonia unsuccessfully treated as outpatients and hospitalised at the Department of Paediatric and Allergy during the infectious season of 2015–2016. In this period of time, 507 patients at the age from 5 weeks to 17.5 years were hospitalised. Pneumonia caused by Mycoplasma pneumoniae and Chlamydophila pneumoniae was confirmed by the presence of IgA and/or IgM antibodies (positive result >1.1 RU/mL), and infection caused by Bordetella pertussis – by IgA antibodies in the serum (positive result >2 IU/mL). Most of the patients had chest X-ray performed. Mycoplasma pneumoniae and/or Chlamydophila pneumoniae were detected in 51 children, and pertussis – in 131 children. Patients admitted to hospital usually presented lung signs on auscultation such as wheezing, crepitation and rales; some of them also presented rash and fever. The radiological image indicated densities depending on interstitial, parenchymal or mixed changes. Fever and rash usually occurred in younger children (2.5% and 5%, respectively), whilst 38% of patients did not present with auscultatory signs or fever at admission (mainly older children). This study reveals that clinical symptoms of atypical and pertussis-related infections can be very uncharacteristic, and delay in making a proper diagnosis results in improper treatment.