The mechanism of extrusion and intrusion formation in Co-Cr-Mo-N alloys during fatigue deformation was investigated. In particular, we focused on the role of the strain-induced martensitic transformation (SIMT), which is the transformation of the metastable γ face-centered cubic (fcc) phase into a stable ε hexagonal close-packed (hcp) phase at room temperature because of the gliding of Shockley partial dislocations in the γ-phase matrix. We found that the SIMT also plays a crucial role in the formation of extrusions and intrusions. Further, the morphology of the extrusions and intrusions formed in the Co-Cr-Mo-N alloy specimens was very different from that seen in other fcc alloys. The extrusions and intrusions were formed by the gliding of perfect dislocations with a Burgers vector of perfect <a> dislocation on the basal plane of the ε-hcp phase. This suggests that the ε-phases introduced by the SIMT can deform readily.