Introduction: Protein energy malnutrition (PEM) is a global problem among children. Worldwide, 27% of children under five are malnourished. PEM is more common in Pakistan, where nearly half (47%) of children are underweight. Assessment of PEM has traditionally been clinical, which is time-consuming and skill-dependent, with high inter-observer variability. Accordingly, biochemical markers such as serum protein and albumin measurements can be used to assess the nutritional status. At the same time, there is controversy as to whether edema can be considered a reliable clinical marker of hypo-albuminemia. Readily available and reliable tests can often detect nutritional deficiencies before they adversely affect biological function, and certainly before deficiencies can be detected by physical examination. Aims and Objectives: The study aimed to assess PEM in children using biochemical markers such as serum protein, albumin and protein electrophoresis, and to establish a correlation between edema and hypo-albuminemia. Materials and Methods: This analytical clinical study was conducted at the Pediatric Unit-II of Nishtar Hospital Multan for one-year duration from November 2019 to November 2020. The study material included 50 cases of PEM and 20 normal, healthy children. Result: In the PEM cases, total protein and serum albumin were found to be significantly lower compared to normal healthy controls. In this way, total protein and serum albumin can become useful indicators of the nutritional status of malnourished children and good markers of PEM. The albumin and beta fractions in serum protein electrophoresis were significantly lower, while the alpha1, alpha 2 and gamma globulin fractions were significantly higher in malnourished children compared to the control group. Key words: PEM, biochemical markers, serum protein, hypoalbuminemia, electrophoresis, edema