Magnetohydrodynamic (MHD) induced energetic ion loss in neutral beam heated H-mode discharges in the National Spherical Torus Experiment (NSTX) is discussed. After H-mode onset, the neutral particle analyser (NPA) spectrum usually exhibits a significant loss of energetic ions mainly for E > Eb/2 where Eb is the beam injection energy, although this loss occasionally extends to lower energy. The magnitude of the energetic ion loss diminishes with increasing tangency radius of the NPA sightline, increasing the toroidal field and the neutral beam injection energy. Modelling suggests that MHD-induced ion loss is enhanced during H-mode operation due to an evolution of the q and beam deposition profiles that feeds both passing and trapped ions into the region of the plasma affected by the low-n MHD activity. It must be emphasized that this loss mechanism is a pressure profile effect that can sometimes occur in unusually high density L-mode discharges, but almost always is observed in H-mode discharges because of the intrinsic broad electron density profile. Analysis of the particle interaction with a model magnetic perturbation supports the energy selectivity of the observed MHD-induced loss. Transport analysis using a fast-ion diffusion model to emulate MHD-induced energetic ion loss shows significant modifications of the heating produced by the neutral beam which changes the inferred power balance, thermal diffusivities and the thermal energy confinement time. In the case cited herein, MHD-induced energetic ion loss increased the thermal energy confinement, τE, by ∼15% and reduced the toroidal beta, βT, by ∼7%. An accounting of energetic ion loss is therefore important for proper analysis of power balance and transport in plasmas exhibiting MHD-induced energetic ion loss.