Newborns with jaundice requiring or not requiring phototherapy (PT) are at greater risk of developing asthma later in life. In this study, we investigated the effect of PT treatment on eosinophil and eosinophilic cationic protein (ECP) levels in newborns with severe hyperbilirubinemia. Thirty newborns diagnosed with severe hyperbilirubinemia and exposed to light-emitting diode (LED) PT were enrolled into the study. Total serum bilirubin (TSB) levels, complete blood count and serum ECP concentrations were measured before and after PT. TSB and hemoglobin (Hb) counts were lower after PT (p = 0.001). There was no difference between leukocyte, lymphocyte, neutrophil and platelet count before and after PT. Eosinophil levels were increased after PT, although not significantly. ECP levels were higher after PT (p = 0.006). It may be speculated that newborns treated with LED PT, increased ECP might play a role in developing allergic diseases later in life.