The aim of the study was to establish the frequency of hypovitaminosis D in children with type 1 diabetes mellitus (T1D), its influence on biochemical and densitometric parameters and the relation to diabetic nephropathy. 58 children with T1D at the age 9–19 years were enrolled to the study. Vitamin D concentration less than 30 ng/ml was considered as insufficient. 37 children (63.79%) had vitamin D level under 30 ng/ml, from these 19 subjects (32.7%) had vitamin D level under 20 ng/ml and 2 subjects (3.44%) under 10 ng/ml. Children with vitamin D deficiency had significantly lower magnesium concentration and lower Z score of lumbar spine (−1.34 ± 1.24 vs. −0.30 ± 1.21, p = 0.01) compared to diabetics with sufficient vitamin D concentration. No significant difference was found in parameters calcium, phosphorus or glycosylated hemoglobin. Patients with diabetic nephropathy (n = 18) showed no significant difference in vitamin D, glycosylated hemoglobin or Z score of lumbar spine compared to the patients without nephropathy (n = 40). Subjects with nephropathy had significantly longer diabetes duration, significantly higher cholesterol and triacylglycerol concentration. In our cohort of patients nearly two thirds of children had insufficient vitamin D concentration what supports the need to monitor and eventually supplement vitamin D in T1D subjects.