Aero-engine manufacturers are continuously striving to improve component performance and reliability while seeking to increase the efficiency of manufacturing to reduce costs. Efficiency gains by using higher rates of material removal, however, can be counter-productive if they give rise to surface anomalies that distort the material microstructure and reduce the resistance of the material to fatigue crack nucleation. This paper investigates the effect of hole making processes and parameters on surface integrity and the initiation of cracks from low-cycle fatigue (LCF). It reports the dependence of elevated temperature (600 °C) low-cycle fatigue performance of nickel alloy RR1000 from surfaces produced from hole making and subsequent surface conditioning. As-machined surfaces include a reference “damage-free” surface, and two distorted microstructures: (i) a white layer, produced to a depth of 5 and 10 μm and (ii) a distorted gamma prime (γ') structure, produced to a depth of 10 and 15 μm. The effect of shot peening damage-free and 10 μm deep white layer surfaces was also evaluated. It was found that the presence of white layer significantly reduced fatigue performance compared with that shown by the damage-free surface, regardless of whether the white layer was subsequently shot peened or not. In contrast, surfaces showing distorted γ' structures produced much less debit in fatigue life and only from a depth of 15 μm. These results have been rationalized from an examination of fracture surfaces and from measurement of residual stresses before and after fatigue testing. This research is of particular importance as it is among the few reports that quantify the effect of different levels of work piece surface integrity on the fatigue life of a nickel-based superalloy that has been developed for critical rotating components in aero-engine applications.