Remote laser beam cutting is a non-contact, tool-wear-free cutting technology that guarantees consistent cutting quality for fiber-reinforced polymers with high efficiency. Since it is a thermal process, a heat-affected zone (HAZ) inevitably occurs at the edge of the cut. Within this HAZ the original material condition is changed locally, which influences the mechanical behavior of the component. In this paper, we have investigated the effect of HAZ on fatigue behavior, for the first time, using a high-resolution X-ray Computed Tomography (XCT) for carbon fiber reinforced polymer (CFRP). The investigation methodology allows non-destructive diagnostics of the HAZ. The laser-cut materials were compared to those machined by conventional milling. The quantitative damage mechanisms, in terms of delaminations, transverse cracks, etc., were investigated and correlated to the laser and milled processes.