Previous studies of the interaction between boundary layer streaks and Tollmien-Schlichting (TS) waves have shown puzzling effects. Streaks were shown to reduce the growth rate of primary TS waves and, thereby, to delay transition; however, they can also promote transition by inducing a secondary instability. The outcome of the interaction depends on the spanwise wavelength and intensity of the streaks as well as on the amplitude of the TS waves. A Floquet analysis of secondary instability is able to explain many of these features. The base state is periodic in two directions: it is an Ansatz composed of a saturated TS wave (periodic in x) and steady streaks (periodic in z). Secondary instability analysis is extended to account for the doubly periodic base flow. Growth rate computations show that, indeed, the streak can either enhance or diminish the overall stability of the boundary layer. The stabilizing effect is a reduction in the growth rate of the primary two-dimensional TS wave; the destabilizing effect is a secondary instability. Secondary instability falls into two categories, depending on the spanwise spacing of the streaks. The response of one category to perturbations is dominated by fundamental and subharmonic instability; the response of the other is a detuned instability.