Strong deep eddies with cyclonic vorticity greater than 0.2 f0 were detected using an array of bottom current and pressure measurements in the Kuroshio Extension System Study (KESS) in 2004–2006. Daily maps showed these deep eddies developed locally. As in the Gulf Stream, meandering of the upper baroclinic jet generates deep cyclones and anticyclones by stretching and squashing the lower water column. However, unlike the Gulf Stream, the smaller vertical stretching and greater water depth in the Kuroshio Extension limits the relative vorticity generated by this vertical coupling process to about 0.1 f0. In the deep Kuroshio Extension the strong cases of vorticity generation and cyclone development are related to stretching driven when water columns are advected off isolated seamounts in the region. The large observed values of relative vorticity are consistent with a straightforward calculation of deep layer potential vorticity conservation.A barotropic model is used to illustrate the topographic generation of cyclones by ambient currents in synoptic eddies. Positive potential vorticity filaments also develop during the cyclogenetic process with width LR = O(20 km), where LR is the topographic Rhines scale, and travel anticyclonically around the seamount. Observational evidence lends support to the existence of submesoscale filaments, insomuch as current meter records near the flanks of seamounts exhibited bursts of eddy kinetic energy when bandpass-filtered between the inertial period and eight days.