Recent concern about gene flow from transgenic plants to weedy species has attracted much research on the fitness of their hybrids. However, no studies have been reported on the very early effects of the seed size of hybrids compared with parental plants for germination, seedling establishment and plant growth. We produced hybrids between male sterile Brassica napus L. (oilseed rape) and five weedy relatives, including Brassica juncea (L.) Czern, B. nigra (L.) Koch, B. rapa L., Hirschfeldia incana (L.) Lagrèze-Fossat and Raphanus raphanistrum L. The hybrid seeds formed between B. napus and B. rapa varied in size, while all the hybrid seeds formed with the other species were small. In a direct-seeded field experiment, small seeds of both parents and hybrids had a lower frequency of emergence and a lower seedling survival rate than large seeds, and resulted in later flowering with less biomass. However, no difference was recorded in a transplant experiment, indicating that growth in the juvenile period was sensitive to the small seed class in field conditions only. The optimum environmental conditions in the greenhouse probably homogenized the developmental differences observed at the early stage, and thus reduced the variation during subsequent growth in the field. This point has not been, but should be, considered in risk assessment of transgenic plants. The lower seedling establishment of small-seeded hybrids could hamper further gene flow.