Background : Protein Energy Malnutrition (PEM) is associated with various changes in the body systems including changes in the haematologic system. These changes affect all the blood cells.. Observations about haematological changes in this group of children have been inconsistent due to frequent and constant changes in haemopoesis resulting from this condition. This has limited the usefulness of these parameters in the anticipatory care of these patients thus the need to describe and validate the changes and possible haematological disturbance among children with PEM informed this study in Ilorin, North-central Nigeria. Methodology : All children admitted into the Emergency Paediatric Unit (EPU) with a diagnosis of PEM were enrolled over a period of one year (January – December 2009). Controls were well children attending the routine clinic without haematologic or infectious condition. Haematological profiles were determined using auto-analyzer SMX 60. Data entry and analysis were carried out with a micro-computer using the Epi info version 3.5 (2008) software packages and p value of < 0.05 was regarded as significant. Results : Ninety children with PEM and 90 age and sex matched controls were studied. Children with PEM had lower mean values for haemoglobin, haematocrit and mean corpuscular haemoglobin (p<0.05) when compared with controls. The mean value of WBC in the children with PEM was 12.8±11.6 ×10 3 cell/mm 3 while it was 5.9±8.7 ×10 3 cell/mm 3 among the controls(p= 0.001). The mean value of platelet counts were 291.8 ±131.7 × 10 9 / L and 326.4 ±133.9× 10 9 / L for the subjects and controls respectively (p=0.0001). A statistical significant difference was observed in the lymphocyte count of the various classes of PEM with the edematous forms having higher counts (p= 0.0001). Conclusion / Recommendation : In conclusion, Children with Protein Energy Malnutrition had lower red cell indices and platelet count, and a higher white cell count than the co