Polyglutamine tract-binding protein 1 (PQBP1), an intellectual disability causative gene, is involved in transcriptional and post-transcriptional regulation of gene expression in animals, and possibly also in plants. In our previous work, reduced brain size, associated with an elongated cell cycle duration in neural stem cells (NSCs), was observed in the NSCs conditional Pqbp1 gene knockout (cKO) mice, which mimic microcephaly patients. However, the physiological significance of PQBP1 in bone metabolism has not been elucidated. Here, we analyzed the bone phenotype of nestin-Cre Pqbp1-cKO mice. Surprisingly, the Pqbp1-cKO mice were significantly shorter than control mice and had a lower bone mass, shown by micro-computed tomography. Furthermore, bone histology showed impaired bone formation in the Pqbp1-cKO mice as well as a chondrocyte deficiency. Real-time PCR analysis showed reduced osteoblast- and chondrocyte-related gene expression in the Pqbp1-cKO mice, while the osteoclast-related gene expression remained unchanged. These results suggest that PQBP1 in bone marrow mesenchymal stem cells may play a crucial role in bone formation and cartilage development.