Abstract The Seed Health Unit of the International Rice Research Institute (IRRI) conducts seed quarantine tests of incoming and outgoing rice seeds. Forty‐eight percent of the incoming shipments did not carry the necessary phytosanitary certificate from the point of origin. Fifteen percent of the incoming rice seed shipments and 0.3% of the outgoing rice seed shipments were contaminated with weed seeds. Twenty weed species were identified as rice seed contaminants. Echinochloa spp. were the most frequent, with as many as 436 seeds per seed‐lot. Storage fungi Penicillium spp., Aspergillus sp. and Rhizopus sp. were detected in incoming Echinochloa spp. weed seeds. Pathogenic seedborne fungi such as Bipolaris oryzae and Fusarium moniliforme were detected from IRRI field‐collected Echinochloa spp. seeds. More care in processing rice seeds for germplasm exchange is needed to prevent weed seed contamination and spread.