Viral respiratory tract infections (VRTI) after hematopoietic stem cell/ bone marrow transplantation (HSCT) are associated with severe morbidity and mortality. Although protective measures have been increased from VRTI for HSCT patients in recent years, these infections are still a serious problem. Treatment regimens which applied for preparation of HSCT and immunosuppressive treatments, used to prevent graft versus host disease (GVHD), especially in patients who underwent allogeneic stem cell transplantation, can lead to suppression of the patients immune system and become more sensitive to the respiratory viral infectious agents. Early diagnosis and treatment are very important because they can prevent serious complications which can cause of these infections and ensure the infection control measures. Nucleic acid-based tests have begun to use widely in recent years, have provided rapid, accurate and reliable diagnosis of respiratory viral infectious agents. In particular, with the introduction of the multiplex molecular assays that able to simultaneously detect many pathogens, has facilitated the diagnosis of some pathogens which couldn't detected by conventional methods previously. In this article, VRTI, and viral respiratory infections agents encountered in HSCT performed children are presented as a literature review.