Crossflow instability of a three-dimensional boundary layer is a common cause of transition in swept-wing flows. The boundary-layer flow modified by the presence of finite-amplitude crossflow modes is susceptible to high-frequency secondary instabilities, which are believed to harbinger the onset of transition. The role of secondary instability in transition prediction is theoretically examined for the recent swept-wing experimental data by Reibert et al. (1996). Exploiting the experimental observation that the underlying three-dimensional boundary layer is convectively unstable, non-linear parabolized stability equations are used to compute a new basic state for the secondary instability analysis based on a two-dimensional eigenvalue approach. The predicted evolution of stationary crossflow vortices is in close agreement with the experimental data. The suppression of naturally dominant crossflow modes by artificial roughness distribution at a subcritical spacing is also confirmed. The analysis reveals a number of secondary instability modes belonging to two basic families which, in some sense, are akin to the ‘horseshoe’ and ‘sinuous’ modes of the Görtler vortex problem. The frequency range of the secondary instability is consistent with that measured in earlier experiments by Kohama et al. (1991), as is the overall growth of the secondary instability mode prior to the onset of transition (e.g. Kohama et al. 1996). Results indicate that the N-factor correlation based on secondary instability growth rates may yield a more robust criterion for transition onset prediction in comparison with an absolute amplitude criterion that is based on primary instability alone.