Purpose: To evaluate the clinical characteristics of vitamin D deficiency and its association with iron deficiency anemia (IDA). Methods: A total of 171 children aged less than two years underwent 25-hydroxyvitamin $D_3$ tests between January 2007 and July 2009. The study was classified into two groups: normal and vitamin D insufficiency, by their vitamin 25-hydroxyvitamin $D_3$ levels. Results: In total, 120 children were in the normal group (mean age, body weight and heights $12.5{pm}7.0$, $9.3{pm}0.9$ kg and $76.8{pm}1.1$ cm), and 51 children in the vitamin D insufficiency group ($9.9{pm}5.4$ months, $9.0{pm}0.9$ kg and $75.1{pm}0.9$ cm). Vitamin D insufficiency was most commonly diagnosed in the spring (44%). The proportion of complete breast-feeding was higher in the insufficiency (92%), and 25.5% of the children in the deficient group also experienced IDA compared that 12% of normal group. Ten children in the insufficiency group experienced bony changes. Six children received calcitriol medication in the normal group, in whom the mean vitamin 25-hydroxyvitamin $D_3$ level increased from $39.6{pm}14.6$ ng/mL (pre-medication) to $41.8{pm}17.2$ ng/mL (post-medication), and 13 in the insufficiency group, in whom the mean vitamin 25-hydroxyvitamin $D_3$ increased from $20.7{pm}7.0$ ng/mL to a mean post-treatment level of $43.7{pm}23.8$ ng/mL. Conclusion: This study demonstrated that approximately 30% of children aged ${leq}2$ years experienced vitamin D insufficiency associated with subclinical rickets. Many children also experienced concurrent IDA. Guidelines for vitamin D supplement in such children must therefore be established.