Objectives: to evaluate the effect of percutaneous autologous bone marrow derived stem cells grafting to treat the long bone diaphyseal nonunions. Materials and methods: from January 2009 to November 2011, 41 patients with nonunions of long bone were treated with percutaneous drilling and autologous bone marrow derived stem cells grafting. They were evaluated the healing result and the relation with the number of bone marrow cells: CD34+, CD 73+ stem cells in Institute of Orthopaedic-Traumatology, Viet-Duc Hospital and Department of Immunology-Cytogenetic and Molecular Biology National Institute of Hematology and Blood Transfusion of Vietnam. Results: None of the patients had post-op complications. Bone union was obtained in 37 patients (90.24 percent) at an average of 24 months follow up. The bone marrow grafts used for these patients contained a mean of l2.45 + or - 8.17 x 10 exponent 6 CD34(+) stem cells and 9.73 + or - 3.21 x 10 exponent 6 CD73(+). There was a positive correlation between the time healing and callus level and the number of stem cells in the graft. Conclusions: Percutaneous autologous bone marrow derived stem cells grafting is a minimally invasive alternative, effective and safe method for the treatment of the long bone diaphyseal nonunions with the comparative bone healing rate.