Even though limited evidence is available, the relationship between morbidity and under-nutrition among children under-five is likely to be a strong two-way association. This study aims to explore this vicious cycle by employing longitudinal data of four periods within a 24 month follow-up, whereby morbidity was captured between two subsequent anthropometric measures. Malnutrition was classified according to z-scores of anthropometric measures and morbidity by number of sick days experienced inbetween. Mixed-effects models were used to assess this relation, where dependency of morbidity and nutritional status were interchanged; models were adjusted for province, age, gender, wealth index score, maternal education level, diet, and Water, Sanitation, and Hygiene indicators. Stunting and wasting prevalences were 29.9% and 8.9%, respectively, where 21.3% of the children hadmultiple anthropometric failures. Children identified as wasted were 35% more likely to experience prolonged illness periods (OR: 1.35, 95% CI: 1.02–1.56). Those experiencing high proportion of sick days were found to be 64% more likely to become stunted (OR: 1.64, 95% CI: 1.18–2.29). This study suggests that the link between wasting and stunting could be partly explained by acute illness, where wasting increases the likelihood of prolonged epiosed of illness, which increases the risk of stunting.