Myelodysplastic neoplasms (MDS) are heterogeneous neoplasms that originate from bone marrow (BM) hematopoietic stem cells. S100A8 and S100A9 (S100A8/9) are crucial molecules involved in the innate immune pathogenesis of MDS. This study aimed to explore the value of these molecules in the differential diagnosis of MDS, and analyze the correlations between their concentrations and clinical characteristics.We measured the concentrations of S100A8/9 in BM supernatant from patients newly diagnosed with MDS (n = 80) or aplastic anemia (AA) (n = 26) by enzyme-linked immunosorbent assay (ELISA). Correlations between clinical characteristics and S100A8/9 were explored based on patients' clinical information.Our study found the concentrations of S100A8/9 in the BM supernatant of MDS patients were significantly higher than those in AA patients (Both P < 0.05). The concentrations of S100A8/9 in the group of very low/low/partial intermediate (IPSS-R score ≤ 3.5) risk MDS patients were also higher than those in AA patients (Both P < 0.05). The serial or parallel diagnostic tests combining these two molecules for differentiating IPSS-R score ≤ 3.5 MDS and AA yielded high positive or negative predictive values, respectively. Moreover, the concentrations of S100A8/9 in MDS patients were positively correlated with the patients' age and the proportion of granulocytic series in BM (All P < 0.05). Meanwhile, the concentrations of the two molecules had significantly negative correlations with the proportion of erythrocytic series in BM (Both P < 0.05). However, intergroup differences in concentrations of S100A8/9 were not significant among different MDS risk groups, whether by IPSS-R or IPSS-M (All P > 0.05).The concentrations of S100A8/9 in BM supernatant have potential value in the differential diagnosis of MDS and AA. The correlations between the molecules' concentrations and clinical characteristics could provide new perspectives for future research in MDS.Copyright © 2025 Elsevier Ltd. All rights reserved.