Vitamin D deficiency in children is a common nutritional issue in many populations worldwide, associated not only with skeletal malformations but, as recent studies suggest, also with the development of obesity and metabolic syndrome. The aim of this observational study was to assess the nutritional status of vitamin D in a group of Polish children with obesity and different grades of metabolic syndrome, with a consequent analysis of the correlation between vitamin D levels and the components of metabolic syndrome. For that purpose, the group of 78 participants (mean age: 14.18 ± 2.67 years) was recruited and further grouped in relation to vitamin D status into two groups of children with and without vitamin D deficiency. The biochemical parameters associated with obesity as well as anthropometric measures were assessed and analysed in search of significant differences between the groups. In the current group of children with obesity and vitamin D deficiency, HDL (45.00 ± 9.29) and adiponectin (7.21 ± 1.64) were found to be significantly lower than in their peers without vitamin D deficiency, whereas W/HtR (0.60 ± 0.04) and TG (171.31 ± 80.75) levels proved to be significantly higher. Body composition analysis using bioelectrical impedance returned no significant findings. The above findings suggest that vitamin D deficiency may influence lipid and glucose metabolism in children, leading to the development of abnormalities characteristic of the metabolic syndrome. A W/HtR parameter was shown to be a sensitive marker of abdominal obesity, which might provide an important means of assessing the correlation between vitamin D and this type of obesity. Independently, vitamin D deficiency may also influence the endocrinological function of adipose tissue, leading to lower concentrations of adiponectin. These in turn presented a linear correlation with the high results of the OGTT in the second hour of the test, hinting at its potential role in the pathophysiology of insulin resistance.