BACKGROUND: Acute malnutrition is one of the main causes of morbidity and mortality among children under 5 years worldwide, and Action Contre la Faim (ACF) aims to address its causes and consequences. To better tailor humanitarian programs, ACF conducts standardized contextual studies called Link NCAs (Nutrition Causal Analysis), to identify factors associated with severe acute malnutrition (SAM) and moderate acute malnutrition (MAM). Data from three Link NCAs performed in 2018 and 2019 in Haiti, Burkina Faso and Madagascar were used to explore the prevalence of malnutrition by different indicators and associated risk factors among children aged 6-59 months. METHODS: Cross-sectional data, collected via household surveys applying two-stage cluster sampling, were pooled to build a sample of 1,356 children. Recommended anthropometric thresholds were used to define SAM (Weight-for-Height Z-score (WHZ) <-3 or Mid-upper Arm Circumference (MUAC) <115 mm and/or presence oedema), MAM (-3≤WHZ<-2 or 115≤MUAC<125 mm) and global acute malnutrition GAM (SAM or MAM) among children. Multivariate analyses for each anthropometric indicator were performed using logistic mixed models and adjusting for potential confounders. RESULTS: The prevalence of acute malnutrition was the highest in Madagascar. The risk of having GAM and MAM varied across countries, while the risk of having SAM varied across clusters. Being male, suffering from diarrhea, and having unwashed face and hands, were significantly associated with GAM by WHZ with adjusted odds ratio of 1.9 [95%Confidence interval (CI):1.1-3.2], 1.7 (95%CI: 1.0-3.1) and 1.9 (95%CI: 1.0-3.6) respectively. These factors were also associated with MAM by WHZ. None of the studied factors was significantly associated with SAM, which could be due to a small sample size. CONCLUSION: These results obtained from a large sample contribute to the evidence of the factors associated with undernutrition in children aged 6-59 months. Further research with larger sample sizes is needed to confirm these results.