Abstract In this paper, a new theoretical model is developed, based on the modified couple stress theory, for the vibration analysis of fluid-conveying microtubes by introducing one internal material length scale parameter. Using Hamilton's principle, the equations of motion of fluid-conveying microtubes are derived. After discretization via the Differential Quadrature Method (DQM), the analytical model exhibits some essential vibration characteristics. For a microtube in which both ends are supported, it is found that the natural frequencies decrease with increasing internal flow velocities. It is also shown that the microtube will become unstable by divergence at a critical flow velocity. More significantly, when the outside diameter of the microtube is comparable to the material length scale parameter, the natural frequencies obtained using the modified couple stress theory are much larger than those obtained using the classical beam theory. It is not surprising, therefore, that the critical flow velocities predicted by the modified couple stress theory are generally higher than those predicted by the classical beam theory.