Hematopoietic stem cell transplantation (HSCT) recipients frequently develop opportunistic infections, including paranasal sinusitis. Paranasal sinusitis in post-transplant recipients can be complicated by life-threatening infections. Accordingly, we analyzed risk factors for development of paranasal sinusitis following HSCT and reviewed our experiences for analysis of the role of management of paranasal sinusitis prior to HSCT. A retrospective review was performed for patients who had received HSCT at Samsung Medical Center (Seoul, South Korea) from 1996 to 2003. A total of 252 patients were analyzed. While 23 patients (9.1%) had sinusitis prior to HSCT, its occurrence rate increased to 15.9% after HSCT. Patients with pre-HSCT sinusitis showed a high occurrence rate of post-HSCT sinusitis (34.8 vs. 14.0%, p = 0.015). However, when pre-HSCT radiological abnormality alone was compared to no evidence of sinusitis prior to HSCT, there was no significant difference in the occurrence rates of post-HSCT sinusitis (15.6 vs. 12.8%, p = 0.541). Although statistical significance was not demonstrated, the occurrence rate of post-HSCT sinusitis was relatively low in patients who received autologous HSCT compared to those who received allogeneic HSCT (11.3 vs. 20.3%, p = 0.060). Use of total body irradiation and presence of graft-versus-host disease did not correlate with development of post-HSCT sinusitis. Compared to the observation group, occurrence of post-HSCT sinusitis showed a slight reduction with medical or surgical intervention targeting radiological abnormalities of the paranasal sinuses (10.0 vs. 25.0%, p = 0.057). In conclusion, pre-HSCT sinusitis and allogeneic HSCT are associated with development of post-HSCT sinusitis. Although asymptomatic radiological abnormalities of the sinus do not increase the risk of post-HSCT sinusitis, optimal treatment prior to HSCT tends to decrease the risk of post-HSCT sinusitis.