We consider the convective instability of stationary and traveling modes within the boundary layer over a disk rotating in a uniform axial flow. Complementary numerical and high Reynolds number asymptotic analyses are presented. Stationary and traveling modes of type I (crossflow) and type II (streamline curvature) are found to exist within the boundary layer at all axial flow rates considered. For low to moderate axial flows, slowly traveling type I modes are found to be the most amplified, and quickly traveling type II modes are found to have the lower critical Reynolds numbers. However, near-stationary type I modes are expected to be selected due to a balance being struck between onset and amplification. Axial flow is seen to stabilize the boundary layer by increasing the critical Reynolds numbers and reducing amplification rates of both modes. However, the relative importance of type II modes increases with axial flow and they are, therefore, expected to dominate for sufficiently high rates. The application to chemical vapour deposition (CVD) reactors is considered.