© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons LtdIron and vitamin B12 deficiencies are two of the most common diseases in the childhood group. Deficiencies of iron and vitamin B12 affect many systems in the body. In this study, to discover the effects of iron and vitamin B12 deficiencies on the hematopoietic stem cells, we studied CFU assay from peripheral blood. One hundred and two children were included in our study and were evaluated in five categories: iron deficiency, iron deficiency anemia, vitamin B12 deficiency, iron and vitamin B12 deficiency, and controls. As a result of statistical analysis, no significant difference was detected between five groups in terms of CFU assays. The results of our study suggest that, in emergent situations, stem cell samples can be collected before treatment with B12 or iron which are common deficiencies in donors of hematopoietic stem cell transplantation. We conclude that we could reach more accurate results by designing a study which contains more patients and includes in vivo results.