Mouse models are widely used in the study of musculoskeletal radiobiology both in vivo and in vitro. Two of the most commonly used mouse strains are C57BL/6 and BALB/c. However, little is known about their equivalence in response to ionizing radiation. In this study we compare the responses of marrow stromal cells derived from both of these strains to X rays in vitro at passages 0 and 2. Colony-forming efficiency was significantly higher in BALB/c marrow stromal cells at passage 0. Radiation-induced decreases in colony-forming unit (CFU) formation at passage 0 were comparable across both strains at 0–2 Gy, but BALB/c stromal cells were more radiosensitive than C57BL/6 stromal cells at 3–7 Gy. Osteogenic differentiation at passage 2 was not affected by radiation for either strain. This work demonstrates that commonly used inbred mouse strains differ in their early-passage marrow stromal cell responses to X rays, including self-renewal and differentiation potential. This variability is an important point to consider when selecting an animal model for in vivo or in vitro study.