We investigate the changes to a fully developed turbulent boundary layer caused by the presence of a two-dimensional moving wave of wavelength L = 2π/k and amplitude a. Attention is focused on small slopes, ak, and small wave speeds, c, so that the linear perturbations are calculated as asymptotic sequences in the limit (u* + c)/UB(L) → 0 (u* is the unperturbed friction velocity and UB(L) is the approach-flow mean velocity at height L). The perturbations can then be described by an extension of the four-layer asymptotic structure developed by Hunt, Leibovich & Richards (1988) to calculate the changes to a boundary layer passing over a low hill.When (u* + c)/UB(L) is small, the matched height, zm (the height where UB equals c), lies within an inner surface layer, where the perturbation Reynolds shear stress varies only slowly. Solutions across the matched height are then constructed by considering an equation for the shear stress. The importance of the shear-stress perturbation at the matched height implies that the inviscid theory of Miles (1957) is inappropriate in this parameter range. The perturbations above the inner surface layer are not directly influenced by the matched height and the region of reversed flow below zm: they are similar to the perturbations due to a static undulation, but the ‘effective roughness length’ that determines the shape of the unperturbed velocity profile is modified to zm = z0 exp (kc/u*).The solutions for the perturbations to the boundary layer are used to calculate the growth rate of waves, which is determined at leading order by the asymmetric pressure perturbation induced by the thickening of the perturbed boundary layer on the leeside of the wave crest. At first order in (u* + c)/UB(L), however, there are three new effects which, numerically, contribute significantly to the growth rate, namely: the asymmetries in both the normal and shear Reynolds stresses associated with the leeside thickening of the boundary layer, and asymmetric perturbations induced by the varying surface velocity associated with the fluid motion in the wave; further asymmetries induced by the variation in the surface roughness along the wave may also be important.