Introduction In Lake Chad, a region located on the Sahelian strip, malnutrition is recurrent and constitute a real public health problem. Of children aged 6 to 59 months, 14.7% suffered of global acute malnutrition and 12.6% (95% CI: 10.7%–14.8%) of moderate acute malnutrition (MAM) with a mortality rate of 0.98/10,000 children per day (Smart, 2014). Government, international and non-governmental organizations, adopt policies, deploy resources to fight against malnutrition in Chad and especially in this Region, but the crisis persists [1] . Studies have documented the factors of malnutrition and recognized inadequate nutrition and diseases as immediate causes. Added to this are the underlying causes such as situations of food insecurity, inadequate dietary practices, etc. [2] . However, all these factors occur alone or in aggregate according to specific contexts [Food and Agriculture Organization–World Health Organization (WHO), 1992]. Apart from general descriptive surveys such as Multiple Indicator Cluster Survey (Mics), Food Security Assessment (Ensa), few studies have studied and/or documented specific factors of malnutrition in this region. Therefore, this study aimed to study the factors associated with MAM in children from 6–59 months in the Lake Chad region. Methods This study was conducted from March to April 2015 in six Nutritional Units of Sanitary Districts of Bol and Ngouri, in the Lake Chad Region. This was a matched case-control study for sex and age with a sample of 252 pairs of children aged 6 to 59 months. Anthropometric data of the children were measured. “Cases” were defined for any child, girl or boy whose weight-for-height was between −3 and −2 Z-scores, and without edema (WHO standard included in the 2014 version of the National Management Protocol of Malnutrition in Chad). “Controls” were diagnosed unharmed of malnutrition (acute malnutrition, stunting, overweight or obesity). They live in the social environment as close as possible to the cases (same neighborhood or village). In this work, we studied sociodemographic factors, obstetric factors, dietary and health factors (breastfeeding, dietary diversity score according to the seven food groups - WHO standard, morbidity of the child, nutritional status of the mother), the factors related to the health system, water, hygiene and sanitation. A conditional logistic regression model was used to calculate association measures (adjusted odds ratios: ORa) and their 95% confidence intervals. Results This results focused on the 252 pairs of children included in the study. Our analyzes showed that the odds of malnutrition were four times higher when children's diets were not diversified (consumed food belonging to less than four of the seven food groups) than when it was (ORa = 4.03 [1.86–8.73], P Conclusion This work allowed us to explore and identify the factors associated with MAM in the Lake Chad Region. The results confirm some of our specific hypotheses that, children whose diet was not diversified, those with recent diarrhea and children whose mothers had a Muac less than 210 mm were the most affected by moderate acute malnutrition.