This study was done to investigate the impact of season of operation, age at operation, and surgical era on short-term outcome after single ventricle palliation. One small study suggests that operation during viral respiratory season is associated with prolonged pleural effusion and hospitalization. Single-institution studies also find improved outcomes after the Glenn shunt and Fontan over time, despite operation at a younger age. The Pediatric Cardiac Care Consortium (PCCC) database for Fontan (n = 2,713) and Glenn shunt (n = 2,239) performed between 1982 and 2000 was utilized. Death during initial hospitalization and length of stay after each procedure were investigated. Viral respiratory season was defined as the interval of November to March. The mortality rate after Fontan was higher during the viral respiratory season (14 versus 11%, p = 0.03) and in children under age 2 years. Glenn shunt mortality was higher with operation before age of 120 days, but was not affected by operation during viral respiratory season. Age at operation for the Fontan procedure has decreased with declines in hospital mortality (14% to 7%, p < 0.0001) and hospital stay (14 to 11 days, p < 0.0001) comparing 1992 to 1995 with 1996 to 2000. Fontan procedure performed during viral respiratory season is associated with an increased mortality. Short-term mortality and morbidity after the Glenn and Fontan procedures have improved in the recent era. Operation in the youngest age groups may adversely impact mortality.