Background: Undernutrition is one major public health problem affecting the physical and mental development of infants and young children in Ghana. It is often as a result of inadequate dietary intakes or due to the prevalence of diseases and infections. Inadequate food intake which is a reflection of household food insecurity, improper feeding practices and unhealthy household environment are considered as the underlying causes of undernutrition. Poor household sanitation practices increases the risk of diseases such as diarrhoeal infections in children which impacts negatively on their nutritional status. Objective: To determine the risk factors for undernutrition in children under-five years in Ghana Methods: This was a secondary data analysis of the 2011 Multiple Indicator Cluster Survey (MICS) which included anthropometric measurements of children under five years old. Using the modified UNICEF conceptual framework for undernutrition by Black et al as a guide, the variables of interest were extracted and classified into biological and non-biological variables. Bivariate analysis was done to identify variables that associated with undernutrition, logistic regression models were developed to identify the risk factors for stunting, underweight and wasting. Results: The survey recruited 7550 children, 22.7% were stunted, including 6.8% severely so; 13.4% underweight of which 2.6% were severely so; and 6.2% wasted, of which 1.4% were severely so. Child age, gender, reported size of child birth, breastfeeding status, having diarrhoea or fever in the preceding two weeks, number of children in the household, child had health insurance, household wealth, and ethnicity and religion of household health and region were the risk factors for undernutrition. However, child age, sex and region were the only variables common in all three indicators (stunting, underweight and wasting). Conclusion: Undernutrition Ghana is a multi-sectorial problem relating to health and sanitation services, poverty and regional differences. To further reduce the undernutrition prevalence in Ghana, strategies and intervention should target at building the capacity of health staff and existing health structures, intensifying public health messages on child care, integration and collaboration with key stakeholders in addressing the socio-economic inequalities of households and communities as well as the regional discrepancies.