Background: Malnourished children have lower resistance to infections; they are more likely to die from childhood ailments like diarrhoeal diseases and respiratory infections; and for those who survive, frequent illness sap their nutritional status, locking them into a vicious cycle of recurring sickness, faltering growth and diminished learning ability. Objective: To assess the prevalence, pattern and co-morbidities of malnutrition among under-five children in rural and urban communities of Owerri Capital Territory, Imo State. Methods: A descriptive cross sectional study conducted among under-five children in Owerri from January 2008 to December 2012. A multistage sampling technique was employed to select three hospitals each from urban and rural areas, and the total number of eligible under-five children that attended the child welfare clinics constituted the sample population. The registers were used to trace the case notes and data was extracted using a pretested pro-forma. The study population of 693 comprised of 386 children from the urban and 307from the rural communities respectively. Results: The prevalence of malnutrition was 25.3%, though 26.7% in the urban against 23.5% in the rural participants. Majority of the malnourished 117(66.9%) were from the 0-12 month age bracket. Overall, the observed malnutrition states were underweight (60.6%), overweight (26.9%) and marasmus (12.6%). Comparatively, underweight was significantly more in the rural malnourished (72.2%) than in the urban (52.4%) ( 2 = 6.95, P = 0.01, OR = 0.43, CI = 0.22-0.81), whereas, overweight was significantly more in the urban malnourished (34%) than in the rural (16.7%) ( 2 = 6.47, P = 0.02, OR = 2.57, CI = 1.23-5.40). Marasmus though did not differ significantly. Malaria (40%), pneumonia (20.6%) and diarrhoea (18.9%) were the commonest co-morbidities among the malnourished study population. Among the urban malnourished, however, malaria (38.8%) and pneumonia (26.2%) were the two most prevalent diagnosis at presentation, whereas for the rural, malaria (41.7%) and diarrhoea (25%) were the two most prevalent co-morbidities. Conclusions and recommendations: Malnutrition is still prevalent among the under-five in Owerri. The most vulnerable group was the 0-12months, which calls for greater attention to exclusive breast feeding and weaning with nutrient and energy dense foods, as these are essential to reduce malnutrition in this group. Underweight being more prevalent in the rural malnourished children, points to the challenge of food security which is fundamental for child survival. Overweight being more prevalent in the urban malnourished should engender healthier dietary habits in children from affluent homes by the mothers. Malaria was the most prevalent co-morbidity in both urban and rural malnourished populations; hence more efforts should be directed at malaria control measures.