This study aimed to evaluate the frequency of the diverse causes of iron deficiency (ID) and iron deficiency anemia (IDA) and to investigate the treatment outcomes in children. ID was defined as a serum ferritin level<12μg/L and a transferrin saturation<10%. IDA was established as ID combined with a low hemoglobin level judged by age and gender-specific reference intervals. A total of 116 ID patients were categorized into 4 groups: group I:<2 years old (n=45), group II: 2 to 10 years old (n=13), group III:>10 years old, male (n=18), and group IV: >10 years old, female (n=40). One hundred of them (86.2%) were diagnosed with IDA. The most common causes of ID were inadequate intake in group I (55.6%) and blood loss in groups II (46.1%) and IV (37.5%). Helicobacter pylori-associated ID mainly occurred in children more than 10 years old. Forty-five of 57 (78.9%) IDA patients who had underlying diseases treatment and/or iron supplementation for 3 months recovered their hemoglobin levels (follow-up range: 6–27 mo). In conclusion, the peak incidences of childhood ID were ages under 2 years old and 10–18 years old. Different age groups and sexes showed characteristic etiologies. The outcomes of childhood ID were good.