In nearly all hot ion H modes in JET, a magnetohydrodynamic (MHD) event is clearly observed just before the time the stored plasma energy saturates and the neutron yield starts to decline. The results of a systematic analysis of MHD observations for a large number of discharges is reported. The relationship between MHD phenomena and the onset of confinement limitation is discussed, as are aspects of the three main types of performance limiting MHD: (a) low-n modes in the outer regions of the plasma, (b) sawteeth and (c) giant edge localized modes (ELMs). Model simulations indicate how the transport is affected and allow an assessment of how much the neutron yield would be improved if the MHD activity were absent