<p>An experimental study of the primary and secondary unsteady instability of a swept-wing boundary layer is carried out under conditions of predominance of the primary cross-flow instability in presence of a localized three-dimensional roughness element of the surface. The measurements were carried out by a hot wire in a low-turbulence wind tunnel at a low subsonic incident-flow velocity under conditions of uncontrolled (“natural”) unsteady perturbations. Four types of amplified unsteady boundary-layer disturbances have been found and studied in detail: (i) low-frequency one, associated with primary flow instability, (ii) medium-frequency one (type III of secondary instability), and high-frequency ones, of types I (iii) and II (iv) secondary instabilities. The properties of these disturbances have been studied in detail and an analysis of positions and shapes of regions of their localization (in the wall-normal and flow-normal plane) with respect to the high-shear layers of the streamwise component of mean-flow velocity in spanwise and wall-normal directions have been performed. A complicated nature of the secondary disturbances is shown. This nature is difficult to explain by means of simplified concepts about the existence of the <i>z</i>- and <i>y</i>-modes of secondary instability proposed in previous studies.</p>