A total of 722 rice seed lots were collected at six production regions of Rio Grande do Sul state during three consecutive seasons (2009/10 to 2011/12). For each seed lot, 200 seeds were assessed for the presence of Bipolaris spp. using a standard seed health blotter test. Results showed that B. oryzae and B. cynodontis were found in 62.5% and 10.4% of the seed lots, respectively. Overall mean incidence of B. oryzae and B. cynodontis were 0.5% and 0.06%, respectively. For the two most sampled varieties (75% of the seed lots), IRGA 424 and Puitá INTA CL, mean incidence levels were highest and lowest, respectively. Among regions, infection risk was highest in the southeastern and lowest in the western regions of the state, especially the Fronteira Oeste. The prevalence and the incidence levels of Bipolaris oryzae reported in this study were lower than previous reports in the same region - eighty percent of the seed lots showed incidence levels below the recommended 5% inoculum threshold. In conclusion, rice seeds produced by IRGA-certified growers showed an overall good health quality with regards to B. oryzae infection, which is the main Bipolaris species associated with rice seeds in southern Brazil.