Both bone marrow stromal cells (BMSCs) and transcription factors (GATA-1, GATA-2 and GATA-3) are important in the normal hematopoiesis and the pathogenesis of hematopoietic disease. The purpose of this study was to investigate the expression of GATA-1, GATA-2 and GATA-3 genes in the bone marrow (BM) microenvironment from patients with chronic aplastic anemia (cAA) and normal individuals. Mononuclear cells (MNCs) were isolated from BM of patients with cAA (8 cases) and normal controls (9 cases). Adherent cells (i.e. BMSCs) were collected after long-term culture in vitro. The semi-quantitative expression levels of GATA genes were analyzed by using RT-PCR-enzyme linked immunosorbent assay (RT-PCR-ELISA). The BMSCs with cAA grew slowly compared with the normal BMSCs. In BMSCs, only the expression ratio of GATA-3 gene from cAA group (50.0%) was significant lower than the normal controls (P < 0.05), the expression ratios of other GATA genes from cAA group were similar to the normal controls. There was no difference in the expression level of GATA-1 gene in the BMSCs between normal controls and cAA group. The expression level of GATA-2 gene in BMSCs from cAA was significantly lower than that from normal controls (P < 0.05). The expression level of GATA-3 gene in BMSCs from cAA was significantly higher than that from normal controls (P < 0.05). The dominant expression of GATA-3 gene was found in the BMSCs from cAA and normal controls. GATA genes can be expressed in the BMSCs and may play a role in the regulation of hematopoiesis in normal individuals, as well as in patients with cAA. The change of expression levels of GATA genes may influence the hematopoiesis in BM microenvironment and relate to the pathogenesis and development of aplastic anemia.