Antibiotics are clearly most prescribed drugs in neonatal intensive care units (NICU) today. The primary reason behind antibiotic use is the treatment and prevention of sepsis in infants. Sepsis in infants is divided into two categories - early onset sepsis (EOS) and late onset sepsis (LOS), and there exists a difference in terms of the risk factors and the causative agents related to these two sepsis groups. Preterm infants show especially high risk for development of sepsis. Correctly diagnosing sepsis is a relevant issue due to the unspecificity of its clinical signs. The most commonly used diagnostic methods currently include complete blood count, CRP (C-reactice protein), procalcitonin and hemocultures while some less common methods such as presepsin and PCR (polymerase chain reaction) are also being reserached. Ampicilin and gentamicin are the most commonly prescribed antibiotics in NICUs. Antibiotic prescription is very variable and it differs from medical institution to medical institution. Criteria used for assessing whether to commence antibiotic therapy include evaluation of risk factors which consist of: clinical presentation, weight at birth, degree of prematurity, group B streptococci (GBS) colonisation of the mother, duration of membrane rupture and maternal intrapartal antibiotic prophylaxis. The treatment is generally discontinued after laboratory results demonstrate a calming of inflammation markers. Harmful effects of antibiotics are best divided into those that are immediate and those that are delayed. It is belived that the majority of the harmful consequences of antibiotic treatment comes from their effect on the development of physiological flora. Antimicrobial resistance, increased risk of necrotising enterocolitis (NEC), bronchopulmonary dysplasia, retinopathy and even increased mortality all fall under immediate consequences of antibiotic overtreatment. The most important delayed consequences are the disruption of normal weight gain and asthma. Antibiotic stewardship programs and emphasizing the role of breastfeeding are considered to be important for the decrease of newborn infant exposure to the harmful effects of antibiotic treatment.