Aim of the study: The aim of the study was to assess the clinical utility of inflammatory markers for differentiating the aetiology of diseases associated with fever in children. Material and methods: A retrospective analysis was performed on the medical records of 1,454 children (658 girls and 796 boys) hospitalised at a paediatric department in 2016–2017 for diseases associated with fever. The analysis was performed on the whole study group, which was divided into the following age groups: children in their 1st year of life (n = 422; 29.1%), children between their 2nd and 6th year of life (n = 870; 59.8%) and children from their 7th year onwards (n = 162; 11.1%). The following inflammatory markers were analysed: white blood cell count, C-reactive protein level, procalcitonin level, erythrocyte sedimentation rate and neutrophil-to-lymphocyte ratio. Results: C-reactive protein, erythrocyte sedimentation rate and neutrophil-to-lymphocyte ratio turned out to be useful in the identification of aetiology of upper and lower respiratory tract infections in all children (p < 0.05). Higher inflammatory marker values were observed in compound infections as opposed to single conditions (p < 0.05). C-reactive protein and erythrocyte sedimentation rate were proven to be useful in identifying the aetiology of acute gastroenteritis. A detailed analysis was performed on the group of children in their 1st year of life. It revealed that inflammatory markers were higher for urinary tract infections than for lower respiratory tract infections and gastroenteritis (p < 0.05). Conclusions: Inflammatory markers may be helpful for determining the aetiology of infectious diseases associated with fever in children. However, therapeutic decisions should always be taken based on the complete clinical picture.