In this paper a comparative study is presented to assess the uncertainty of two methods for 3C3D velocimetry in microscopic flows: stereoscopic micro-particle image velocimetry (S-μPIV) and wavefront-deformation, or astigmatism, micro-particle tracking velocimetry (WD-μPTV). First, the main parameters affecting both methods’ measurement uncertainty are identified, described and quantified. Second, the test case of flow over a backward-facing step is analyzed using both methods. For comparison standard 2D-2C μPIV measurements and numerical flow simulations are shown as well. Advantages and disadvantages of both methods are discussed.