Purpose: The increasing prevalence of breast feeding has led to concerns about vitamin D deficiency (VDD) and iron deficiency anemia (IDA) in children. We evaluated the prevalence of VDD in a population of Korean children with IDA and assessed the risk factors for VDD in these children. Methods: A total of 79 children who were diagnosed with IDA were prospectively surveyed from April 2010 to March 2011. Data were collected by questionnaire, medical assessment, and laboratory tests, including measurement of 25-hydroxyvitamin D (25OHD), hemoglobin, and wrist radiography. Results: The median age was 22 months and 30% of the subjects were female. Over a half of subjects (58%) had subnormal vitamin D level (25OHD<30 ng/mL), and VDD (25OHD<20 ng/mL) was present in 39% of children. There was no difference in serum hemoglobin level between IDA patients with VDD and those without VDD. Most subjects (89%) were currently or had recently been breastfed and almost all subjects (97%) who had VDD received breastfeeding. Children with VDD were more likely to be younger than 2 years, to have been breastfed, and to have been tested in winter or spring. Multivariable analysis indicated seasonal variation was a significant independent risk factor for VDD in our IDA patients. Conclusion: Our results demonstrated that VDD has a high prevalence in Korean children with IDA. Primary care physicians should be aware of the possibility of VDD in children with IDA and should supplement the vitamin D as well as iron.