Adequate levels of calcium, phosphate and Vitamin D are essential for bone physiology and growth, as well as preventing some common childhood illnesses. This study aimed to determine the prevalence of the deficiencies of these nutrients and factors affecting their serum levels in Nigerian children. This was a cross-sectional study that involved 220 apparently healthy children aged 6-24 months in Ikenne Local Government Area of Ogun State, Nigeria. Serum calcium and phosphate were assayed using the calorimetric method, while Vitamin D (25-OH Vitamin D) was assayed with ELISA. The mean (±standard deviation [SD]) serum Vitamin D level was 55.07 ± 16.53 ng/ml, while the mean (±SD) serum calcium and phosphate were 2.27 ± 0.13 mmol/l and 1.28 ± 0.18 mmol/l, respectively. Eleven (5%) of the children had hypovitaminosis D, 23 (10.5%) had hypocalcaemia and 12 (5.5%) had hypophosphataemia. Factors found to be significantly associated with hypovitaminosis D included low consumption of milk and the use of a hijab veil, while malnutrition (both undernutrition and overnutrition) was significantly associated with hypocalcaemia. The prevalence levels of hypovitaminosis D and hypophosphataemia were low, while hypocalcaemia was more common. Low milk consumption and use of a hijab veil were risk factors for hypovitaminosis D, while malnutrition was a risk factor for hypocalcaemia. Malnourished children, especially overnourished ones, should be routinely screened for hypocalcaemia because of its high prevalence among them.