Background: Acute Epstein-Barr virus (EBV) infection could lead to atherogenic lipid profile changes in adults; while there is no evidence about the children with Infectious mononucleosis (IM). The aim of this study was to evaluate the lipid profile of the children in acute phase of mononucleosis and two months after the recovery.Materials And Methods: From 2010 through 2012, 36 children with IM aged 1-10 years were enrolled in a prospective cross-sectional study. Fasting serum total cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), and triglyceride level were measured during acute phase of the disease and after 2 months of the recovery.Results: From 36 patients enrolled, 25 (69.4%) cases were male and the mean age of the patients was 4.1 ± 2.0 years. The mean of the total cholesterol level in the acute phase and 2 months after the recovery were149.5 ± 35.3 mg/dL and 145.7±30.6, respectively (P = 0.38). However, the serum level of HDL cholesterol in patients after 2 months of recovery was significantly increased (37.9 ± 9.3 mg/dL vs. 28.5 ± 10.6 mg/dL, P < 0.001). The mean value of serum LDL cholesterol was significantly reduced, two months after recovery (81.4 ± 19.5 mg/dL, vs. 92.6 ± 28.8 mg/dL, P = 0.009). Furthermore, the serum triglyceride level was significantly reduced after the recovery (108.7 ± 36.9 mg/dL) compared with the acute phase (163.8 ± 114.3 mg/dL) (P = 0.004).Conclusion: EBV infection in children could change lipid profile which is partially restored 2 months after the recovery.