The initial growth of a disturbance induced by a near-wall circular cylinder in a flat-plate boundary layer is experimentally investigated using both particle image velocimetry and hydrogen bubble visualization techniques. The secondary spanwise vortices appear in the near-wall region as a direct response to the outside passing wake vortices, consistent with previous studies on similar models (Pan et al., J. ). The streamwise variation of the total disturbance energy within the boundary layer shows a two-stage growth, which characterizes the initial transition process: the first exponential growth stage, followed by a region with slower growth rate. It is revealed that these two stages of growth are related to the formation and the destabilization of the secondary vortex in the near-wall region. The technique of dynamic mode decomposition is used to decompose the total disturbance into temporally orthogonalized modes, and it shows that the first growth stage largely results from the increased disturbance at the same frequency as that of the wake vortex shedding, while the second growth stage comprises the disturbance growth in a number of frequencies, especially the lower ones.