Background: Malaria is an important cause of death and illness in children worldwide. Most cases of neonatal malaria are misdiagnosed because of lack of specific symptoms and general lack of awareness. Nothing much is known in literature about the hematological changes during malaria infection and outcome of disease in neonates. Neonatal malaria is an underdiagnosed entity. So this hospital based observational study aims to assess diagnostic features of neonatal malaria.Methods: From August 2004 to August 2013, information of all slide positive for malaria cases aged 0 to 28 days admitted to our pediatric hospital was collected and analysed. Results: 28 slide positive cases of neonatal malaria were studied, four out of them were congenital malaria. Fever (93%) was the most common symptom followed by pallor (72%) and diarrhoea (50%). We also found respiratory distress in four (14%) cases. Apart from anemia and atypical lymphocytosis, We also found thrombocytopenia and low hematocrit, MCV and RBC count. Two cases with bleeding manifestations expired during course of treatment. Discussion: Malaria in the first few months of life can simulate transplacentally or postnatally acquired infection such as TORCH, syphilis, neonatal hepatitis and septicemia all having an important symptom complex of fever jaundice, hepatosplenomegaly and anemia. Although in our cases clinical presentation has been similar to septicemia but culture of blood, CSF and urine were sterile. The dilemma of distinguishing neonatal malaria alone versus neonatal sepsis or both existing does not seem to be easily resolved by the use of clinical features alone. The laboratory diagnosis of parasitemia in neonates require special attention in Giemsa staining as well as the technical skill involved in malaria microscopy because parasite densities are low. So high degree of suspicion is needed to diagnose malaria in newborns presenting with fever and anemia.