The secondary instability of a zero-pressure-gradient boundary layer, distorted by unsteady Klebanoff streaks, is investigated. The base profiles for the analysis are computed using direct numerical simulation (DNS) of the boundary-layer response to forcing by individual free-stream modes, which are low frequency and dominated by streamwise vorticity. Therefore, the base profiles take into account the nonlinear development of the streaks and mean flow distortion, upstream of the location chosen for the stability analyses. The two most unstable modes were classified as an inner and an outer instability, with reference to the position of their respective critical layers inside the boundary layer. Their growth rates were reported for a range of frequencies and amplitudes of the base streaks. The inner mode has a connection to the TollmienSchlichting (T-S) wave in the limit of vanishing streak amplitude. It is stabilized by the mean flow distortion, but its growth rate is enhanced with increasing amplitude and frequency of the base streaks. The outer mode only exists in the presence of finite amplitude streaks. The analysis of the outer instability extends the results of Andersson et al. (J. Fluid Mech. vol. 428, 2001, p. 29) to unsteady base streaks. It is shown that base-flow unsteadiness promotes instability and, as a result, leads to a lower critical streak amplitude. The results of linear theory are complemented by DNS of the evolution of the inner and outer instabilities in a zero-pressure-gradient boundary layer. Both instabilities lead to breakdown to turbulence and, in the case of the inner mode, transition proceeds via the formation of wave packets with similar structure and wave speeds to those reported by Nagarajan, Lele & Ferziger (J. Fluid Mech., vol. 572, 2007, p. 471).