By using the Stereo Particle Image Velocimetry (PIV) technique we observe the secondary flow of second kind in a corner of a channel of square cross-section. The boundary layer thickness is much lower than the channel size. Therefore, the flow is still developing, not filling the entire channel cross-section, which is the case more widely reported in literature studied in a very long channel. The non-linear secondary effects of interacting boundary layers are observed as a single stream-wise vortex close to the channel corner in case of laminar boundary layers. In the case of turbulent boundary layers, the secondary flow takes shape of a symmetric pair of counter-rotating vortices. This pattern is observable only in the average velocity field, while the instantaneous ones display large amount of vortices, whose spatial distribution close to the corner in dependence on their orientation leads to statistically emergent net vorticity. At the same time, this pattern is reproduced by using a numerical simulation. Display omitted •Secondary flow of second kind in a short channel observed by Stereo PIV•For ReL≤1.0⋅105, the secondary flow is laminar in shape of single vortex in the corner.•The size of laminar secondary flow vortex decreases with ReL as R∼ReL−1∕2.•At ReL≥1.3⋅105, a pair of counter-rotating vortices appears in the averaged sense.•This pattern develops also in a “steady-state” numerical simulation.