This paper aims at understanding the influence of three-dimensional effects in hovering flapping flight. Numerical simulations at a Reynolds number of 1000 are performed to compare two types of flapping kinematics whose plunging phase is characterized by either a rectilinear translation or a revolving motion. In this way, we are able to isolate the three-dimensional effects induced by the free end condition from that induced by the spanwise incident velocity gradient (and the associated implicit Coriolis and centrifugal effects). In the rectilinear translation case, the analysis of the wake and of the aerodynamic loads reveals that the wingspan can be compartmented into three distinct regions whether it is predominantly subjected to an unstable two-dimensional flow, a stable three-dimensional flow or both two-dimensional and three-dimensional effects. It is found that this partitioning exhibits common features for three different aspect ratios of the wing. In conjunction with the previous results of Ringuette, Milano & Gharib (J. Fluid Mech., vol. 581, 2007, pp. 453–468), this suggests that the influence of the tip vortex over the wingspan is driven by a characteristic length scale. In addition, this length scale matches the position of the connecting point between leading and tip vortices observed in the revolving case, providing insight into the connecting process. In both translating and revolving cases, leading edge vortex attachment and strong spanwise velocities are found to be strongly correlated phenomena. Spanwise velocities (that mostly confine at the periphery of the vortices), together with downward velocities, do not only affect the leading edge vortex but also act as an inhibitor for the trailing edge vortex growth. As a consequence, cross-wake interactions between leading and trailing edge vortices are locally limited, hence contributing to flow stabilization.