Aplastic anemia is a syndrome of bone marrow (BM) failure characterized by peripheral pancytopenia and marrow hypoplasia. Its exact pathophysiology is still not clear. Mesenchymal stem cells (MSCs) play an important role in providing the specialized BM microenvironment for hematopoietic stem cells survival and differentiation. MSCs were isolated from BM of five patients with aplastic anemia and five controls. MSCs were characterized by morphology and immunophenotyping. Their viability, proliferative capacity, and adipogenic as well as osteogenic differentiation potentials were assessed. MSCs from aplastic anemia patients and controls shared similar spindle-shaped morphology and surface marker expression. MSCs derived from patients with aplastic anemia showed lower viability (74.2 ± 4.44% vs. 97.0 ± 1.58, p < 0.0001) and slower expansion rate as indicated by smaller population doubling and smaller cumulative population doubling from passages 1 to 4 (0.70 ± 0.22 vs. 2.34 ± 0.84; p = 0.009). Besides, aplastic anemia MSCs had poor capacity to differentiate into adipocytic and osteocytic lineages.