Vitamin D deficiency (VDD) is a public health problem which affects all human beings including darkskinned subjects. In children, it can cause disabilities associated with skeletal abnormalities such as rickets or stunted growth. VDD is also associated with a significant risk of extra-skeletal, infectious, auto-immune, neoplastic, and cardiovascular diseases. The concentration of 25 (OH) D is currently considered as the best VDD indicator. Whereas VDD has been well studied in Western countries and North America, very few studies have been conducted in sub-Saharan Africa. The aim of this study was to assess the prevalence and risk factors of VDD in children aged between 0 to 59 months. This is a cross-sectional prospective study conducted from August 5, 2019, to November 30, 2020. A total of three hundred children were included in this study, two hundred of whom were malnourished and the rest with a normal P/T ratio. The variables studied were vitamin D, serum calcium, magnesium, phosphorus and iron. Ferritin, haemoglobin, protein, albumin and prealbumin were also studied. The prevalence of VDD in the general population was 30%. No significant statistical difference in vitamin D concentration values was noticed between malnourished and nourished children with p = 0.388. Children over 24 months of age are 2.34 times more likely to be VDD than others. Given the prevalence of VDD in the study population, it would be necessary to integrate screening and supplementation into current medical practice.