This study was designed to assess the effect of protein-energy malnutrition (PEM) disease on bone mineralisation. About 20 patients with PEM were enrolled and compared to a cohort of 14 healthy infants. Besides the dietetic history taking, anthropometric measurements and usual laboratory investigations, bone age-estimation and measurement of serum parathyroid and osteocalcin levels were done for patients and controls. Nutritional rehabilitation was supervised for 2–4 months, and the patients were reassessed by the previous clinical, radiological and laboratory parameters. The current study demonstrated decrease in bone age and mineralisation in PEM patients with significant increase in parathyroid hormone and significant decrease in osteocalcin level, both being related to the severity of the condition, yet the bone resorption was more significant than the bone formation. Fortunately, these changes were reversible upon nutritional rehabilitation further emphasising the role of prompt and proper implication of the nutritional rehabilitation programme in PEM patients.