Currently, a gold standard for distinguishing between infectious, inflammatory, auto-immune diseases and malignancy in infants and children is not available. The combination of biomarkers with clinical features and other diagnostic tests could help clinicians in the diagnostic process. Ideally, a biomarker should have high sensitivity, specificity, and predictive value, as well as being easily obtained also in preterm babies and infants, requiring a small amount of blood and being quickly measured. The available literature agrees on the fact that a perfect biomarker is not currently available in paediatric practice. Thus, clinicians must consider time by time the balance between marker characteristics and their sensitivity and specificity in different conditions. The development of new tests with higher sensitivity and specificity in distinguishing different pathological situations is auspicable. Moreover, future efforts should be focused on validating also in children the recently developed biomarkers including CD64, IL-27 and IL-8.