Several prognostic scoring systems have been developed to assess prognosis in myelodysplastic syndrome (MDS). However, currently there are no systems that list gender as a prognostic factor. We queried a National Cancer Institute database to investigate the prognostic influence of gender on the survival of patients with MDS. We first identified 34,681 qualified patients diagnosed with MDS from 2001-2014 in the Surveillance, Epidemiology, and End Results (SEER) database, and then analyzed the characteristics of these patients using chi-squared tests. The Kaplan-Meier method and the multivariate Cox regression model were used to examine whether gender disparity in the survival of patients with MDS existed. We found that male patients had higher incidence rate of MDS (55.3% vs 44.7%, P<0.001) and a significant survival disadvantage (27.6% vs 33.6%, P<0.001) compared to female patients. Moreover, the less favorable survival rate of male MDS patients was associated with the age at diagnosis, race, marital status at diagnosis and the histological subtypes including refractory anemia (RA), refractory cytopenia with multilineage dysplasia (RCMD), myelodysplastic associated with isolated del 5q (MDS 5q-), myelodysplastic/myeloproliferative neoplasm (MDS/MPN) and not otherwise specified (NOS). In conclusion, gender can be considered as an independent prognostic factor for the overall survival of patients with MDS.