The bacterial gene cod A encodes cytosine deaminase (CD), which converts 5-fluorocytosine (5-FC) to 5-fluorouracil (5-FU), a compound that is toxic to cell growth. Consequently, CD can potentially be used as a conditional negative selection marker when 5-FC is applied. Rice seedlings and calli are sensitive to low concentrations of 5-FU, while the substrate of CD, 5-FC, is not toxic. To test whether the cod A gene can be used as a conditional negative selection marker in rice, we developed transgenic rice plants to contain the cod A coding sequence fused with the phloem-specific promoter of rice tungro bacilliform virus. The transgenic rice plants containing the cod A gene can be killed by the addition of 5-FC to the medium. The first generation of rice transgenic lines with the cod A gene showed a 3:1 segregation pattern of 5-FC sensitivity. We therefore conclude that the cod A gene from E. coli can be used as a conditional negative selection gene in rice.