Protein-energy malnutrition (PEM) is a public health problem and is associated with high morbid-ity and mortality. PEM is linked with changes in biochemical and immunological parameters. This study aimed at determining the level of pro-inflammatory cytokines among healthy (control) chil-dren and those with PEM as diagnostic indicators for PEM. The study was conducted between December 2009 and June 2010 comprising a total of 115 children (35 controls and 80 malnourished children) aged between 8 – 36 months attending the Maternal and Child Health Hospital (MCHH), Kumasi. Anthropometric parameters including weight, height and mean-upper arm cir-cumference as well as immunological and biochemical parameters (interleukin-6 (IL-6), tumour necrosis factor-alpha (TNF-α), albumin, total protein) were assessed among the studied population and the control group. After the analysis, 67.5% had marasmus, 18.8% had marasmic kwashiorkor and 13.8% had kwashiorkor. There were no statistically significant differences (p>0.05) in the mean total protein concentration of the subjects before (66.3± 1.6 g L-1) and after (69.6± 1.7 g L-1) nutri-tional supplement when compared to that of the controls (68.37± 1.4 g L-1) . Serum albumin con-centration in the control group (43.2 ± 0.9 g L-1) was significantly higher than the concentration in the subject group before treatment (38.7 ± 0.9 g L-1, p=0.0027). The mean concentration of IL-6 in the subjects at baseline (46.1 ± 7.5 pg mL-1, p=0.0008) and after treatment (26.3 ± 5.2 pg mL-1, p=0.0148) were significantly higher than that in the control group. A 43.8% decrease in the mean concentration of IL-6 was observed after treatment. TNF-α concentration before treatment (82.1 ± 6.0 pg mL-1) was significantly higher when compared to the mean concentration in the control group (55.8 ± 2.2 pg mL-1). The study observed increases in pro-inflammatory response in mal-nourished children with IL-6 concentration being a significant indicator of PEM in the subjects compared to TNF- α.