The treatment of respiratory viruses is extremely challenging in haematopoietic stem cell transplant (HSCT) recipients. Outcomes related to these infections have improved over the past decade. More recently, studies have looked at respiratory virus epidemiology using molecular assays to understand the wide range of diseases in HSCT recipients. The emergence of pandemic H1N1 in 2009 encouraged implementation of molecular assays in many clinical laboratories and broadened influenza resistance detection. Finally, new drugs have been developed to treat influenza virus, respiratory syncytial virus, parainfluenza virus and adenovirus with some promising results.