Abstract The bone marrow stroma, consisting of adipocytes, fibroblasts, and osteoblasts, develops from a multipotent mesenchymal progenitor. The recently described nuclear hormone receptors, known as peroxisome proliferator-activated receptors (PPARs), regulate transcription of genes involved in adipogenesis. Consistent with this is the observation that PPARα-null mice exhibit greater extramedullary adipose stores compared with their wild-type controls. To determine if the status of the PPARα protein also influenced bone marrow stromal cell differentiation, this study compared the frequency of colony forming units for bone marrow adipocytes (CFU-A), alkaline phosphatase-positive fibroblasts (CFU-F/ALP +), and osteoblasts (CFU-O) between wild-type and PPARα-null mice. The CFU frequencies for all lineages were not significantly different in either gender at age 3 weeks, independent of the PPARα background. However, histologic analysis showed that the cross-sectional area of the femur in male PPARα null mice was significantly greater than that of PPARα-null female mice and of both wild-type genders. This was due to an increased marrow cavity space rather than an increased cortical bone area. In addition, while the percentage area of cortical bone occupied by lacunae was equivalent in the PPARα and wild-type males, this value was significantly greater in PPARα-null female mice compared with wild-type females. At age 3–6 months, no significant difference was observed in the CFU-A frequencies, based on either PPARα status or gender. The wild-type male CFU-F/ALP + frequency was significantly greater than the CFU-F/ALP + in all other groups. Although the PPARα status had no influence on the CFU-O frequency, the number of CFU-O was greater in male than in female mice. Sequential incubation of stromal cells in either adipogenic- orosteoblastic-inducing media did not alter the number of CFU-A or CFU-O. These results indicate that the PPARα-null genotype does not influence bone marrow stromal cell numbers.