Abstract Background: A 5-year-old boy with acute lymphoblastic leukaemia (ALL) received a haematopoietic stem cell transplant (HSCT) from his father and was monitored for the presence of respiratory viruses. Study Design: Nasal washes were taken during the transplant period and tested by culture and real-time PCR. Results: Fifteen days prior to transplant parainfluenza virus 3 (PIV3) was isolated by culture and confirmed by immunofluoresence (IF) from a nasal wash specimen. Subsequent samples were negative by both IF and culture so the pre-transplant conditioning was started. One week after the HSCT the patient developed respiratory symptoms which progressively deteriorated. The IF and culture for PIV3 became positive again only after the symptoms deteriorated. However, retrospectively, a real-time PCR assay showed that the PIV3 was detectable throughout the conditioning phase and the amount of virus increased at the time of reappearance of respiratory symptoms post-HSCT. Conclusions: Management of PIV3 infection is important in HSCT. The use of this real-time PCR assay could improve diagnosis and management of PIV3 infection.