Vitamin D (VD) deficiency (VDD) is still a population-based health problem that affects people at different ages. The aim of this study was to evaluate VD prophylaxis for the prevention of VDD in (3-36)-month-old infants and children. Infants and children aged between 3 and 36 months, with different etiologies, admitted to outpatient and inpatient clinics from October 2010 to October 2011 at the Children's Hospital of Erciyes University, were enrolled for the study. Their VD intake (if used; time of initiation, dosage and compliance) and nutritional status (breast-fed, formula or complementary fed) were noted. In order to study seasonal VD changes, the levels of serum calcium, phosphorus and magnesium, alkaline phosphatase activity (PLA), plasma parathyroid hormone (PTH) and 25 hydroxyvitamin 25(OH)D levels were measured at the beginning of VD supplementation during the four seasons. A total of 316 subjects were enrolled in the study, consisting of 202 (63.9%) outpatient and 114 (26.1%) inpatient groups. From these subjects, 304 (96.2%) were supplemented with VD; whereas 12 (3.8%) were not. Out of the subjects supplemented with VD, 237 (75%) initiated VD after the second week of life, 267 (87.8%) were given three drops of VD daily and 209 (66.1%) had taken VD regularly. The plasma 25(OH)D levels were found to be lower in the inpatient group than the outpatient group (29.35 ng/mL and 34.35 ng/mL, respectively). The plasma 25(OH)D levels were lower during the spring and winter. VDD and VD insufficiency (VDI) was found in 31 (9.8%) and 30 (9.5%) subjects, respectively. The plasma 25(OH)D levels were lower in inpatient and breast-fed only subjects and in winter and spring. The national VD augmentation program seems to be beneficial for the prevention of VDD, but VDD/VDI seems to still be an important health problem.