Under continuous rice cropping, open field burning has been the primary means of rice residue disposal and of minimizing the carryover inoculum of Sclerotium oryzae, the cause of stem rot of rice. The phase down of open field burning in California has necessitated the development of alternatives to burning. In 1993, a continuous-year experiment was initiated in Colusa County to evaluate the effects of alternative residue management strategies on overwintering sclerotia of S. oryzae, stem rot incidence and severity, and yield. Treatments were arranged in a split-plot design with winter flooding and winter nonflooding as the main plots, and fall incorporation of the straw residue, rolling of the straw to enhance soil contact, baling and removal of residue, and fall burning as the subplots. S. oryzae inoculum and disease severity were significantly lower and yield was significantly higher in 5 out of 6 years in the winter-flooded main plots compared with the winter nonflooded plots. Over the duration of the trial, S. oryzae inoculum was consistently lower in burn subplots when compared with all other subplots. No consistent differences in disease incidence and severity or yield occurred in the subplots, although average yield over the 6 years was highest in burn subplots when compared with all other subplots. The results suggest that winter flooding is the best alternative to burning for stem rot management.