The acquisition of functional competence represents a critical phase during intrathymic development of T cells. Thymocytes reaching this stage represent cells which have been positively selected on the basis of major histocompatibility complex reactivity, but which have also been purged of potentially autoreactive T-cell receptor specificities by negative selection. While the developmental window in which thymocytes are subjected to positive selection is now well defined, the precise developmental timing of negative selection, in relation to positive selection events, is less clear. Moreover, the underlying mechanism allowing single-positive thymocytes to respond to T-cell receptor ligation by activation rather than death, remains controversial. Here we have analysed the developmental timing of negative selection in relation to positive selection, using measurement of thymocyte susceptibility to dendritic cell presentation of the superantigen staphylococcal enterotoxin B (SEB). We show that thymocytes which have received initial positive selection signals, namely CD4+ CD8+ CD69+ thymocytes, like their CD4+ CD8+ CD69minus sign precursors, are susceptible to negative selection, indicating that induction of positive selection does not convey immediate resistance to negative selection. In contrast, newly generated CD4+ CD8minus sign CD69+ cells are not only resistant to deletion by SEB, but respond to SEB-mediated T-cell receptor-ligation by activation, indicating that the acquisition of functional competence occurs at the newly generated CD4+ CD8minus sign CD69+ stage. Finally, by using direct retroviral infection of primary CD4+ CD8+ thymocytes, we also show that Notch-1 activation in CD4+ CD8+ thymocytes does not correlate with, nor convey resistance to superantigen-mediated negative selection. Thus, our data suggest that although Notch-1 has been implicated in resistance to thymocyte apoptosis, the acquisition of resistance to negative selection occurs independently of Notch-1 signalling.