A bxn gene, coding for the nitilase enzyme that catalyses the detoxification of the herbicide bromoxynil, was inserted into subterranean clover (Trifolium subterraneum L. subsp. yanninicum). The agronomic characteristics of 3 transgenic lines (BXN 5, 7, 10) and their response to herbicides containing bromoxynil, were compared with that of the non-transgenic parent, cv. Gosse, in 1 glasshouse and 2 field experiments.The application of bromoxynil at 1.5 L/ha resulted in a 50% reduction in the spring herbage yield of the non-transgenic control but no reduction in BXN 5 and 7. The level of the phyto-oestrogens, genistein and biochanin A, in the leaf tissue were low in Gosse and the 2 transgenic lines, BXN 7 and 10, but the level of genistein increased significantly (P < 0.05) from 0.85% in Gosse to 1.43% dry weight in BXN 5, and biochanin A increased from 0.35% in Gosse to 0.73% in BXN 5. The application of the herbicides bromoxynil, bromoxynil+MCPA, and Jaguar (bromoxynil+diflufenican) at the cotyledon stage in a glasshouse study significantly reduced the leaf area of the non-transgenic Gosse, but did not reduce the leaf area of the 3 transgenic lines. When applied at the 4–5 leaf stage, the leaf area of Gosse was again reduced by all the herbicides, but only the bromoxynil+MCPA treatment reduced the leaf area of the transgenic lines relative to the control. The application of bromoxynil or Jaguar at the 4–5 leaf stage depressed the herbage yield of Gosse by about 62% compared with 0–24% in the 3 transgenic lines. In the field studies, BXN 5 and 10 had similar seed yields to Gosse in the absence of herbicide application, but the seed yield of BXN 7 was significantly less than the other 2 transgenic lines. The level of hard-seed in BXN 7 was also lower at 25% compared with 55–57% in the other transgenic lines and Gosse.These findings stress the need to carefully assess the agronomic qualities of transgenic lines prior to release as although tolerance to bromoxynil may be greatly increased by the bxn gene, other important agronomic characteristics, such as seed yield, hardseededness, and isoflavone content, may change as result of the gene or transformation process.