Introduction: Nutritional rickets is the visible tip of the iceberg formed by the diseases caused by hypovitaminosis. Vitamin D plasma is essentially influenced by the level of sunlight which is significant in Sub-Saharan Africa and in Benin. However, there are factors likely to impede endogenous production of that vitamin in children in our environment. This research work was conducted with the view to investigate hypovitaminosis D prevalence and associated factors in children aged 6 to 59 months in the District of Parakou in 2017. Methods: This research work was a cross-sectional study with prospective collection of data carried out in community in the District of Parakou in 2017. The study involved euthrophic and non-HIV infected children aged 6 to 59 months who did not benefit from vitamin D supplementation during the past three months. Vitamin D plasma concentration was obtained using “Radioimmunoassay” after cluster random sampling in accordance with WHO guidelines. According to Schwartz formula, nominal minimum sample size was 321. In this study, hypovitaminosis D was defined as a plasma level lower than 30 ng/l. Data processing was carried out using softwares such as EPI INFO version 7.2 and SPSS 21. Results: In total, 400 children were involved in the survey. Hypovitaminosis prevalence was 9.5% (38 out of 400 cases). In our research work, the factors associated with hypovitaminosis were child’s age (p = 0.0470), mother’s age (p = 0.0000), weaning age lower than 6 months (p = 0.0466) and mother’s occupation out of direct sunlight (p = 0.0012). Conclusion: Nearly one out of ten children suffers from hypovitaminosis D in the District of Parakou in 2017. The associated factors were age of child and mother, early weaning and mother’s professional occupation held out of direct sunlight. This research work should be continued and improved by a nationwide multicentre study. This could lead to the adoption of measures for hypovitaminosis D prevention among children in Benin.