Two-dimensional, two-component micron resolution particle image velocimetry (micro-PIV) allows measurement of the in-plane velocity components across a single plane within a micro-scale device. The technique has become well established over recent years for the study of micro-scale flows. Stereoscopic micro-PIV uses two cameras and a stereomicroscope to capture all three components of the velocity field. Recently, preliminary results have been published from stereoscopic micro-PIV systems. Here, a complete validation of a stereoscopic micro-PIV system is carried out by comparing results for flow over a micro step with a computational fluid dynamics (CFD) solution. It is found that the accuracy of the correlation-based PIV technique is limited by the degree of overlap of the two focal planes in the stereomicroscope. This prompts the adoption of a ‘super-resolution’ particle tracking velocimetry (PTV) algorithm, which does not require exact alignment of the two focal planes. The PTV is more accurate than the PIV and systematic deviations near to surfaces are greatly reduced. In addition, since the PTV algorithm tracks the three-dimensional coordinates of individual particles the measured velocities are no longer automatically averaged onto the focal plane of the measurement. Thus the PTV data represent a truly three-dimensional, three-component mapping of the flow field, whose resolution is independent of the microscope lens parameters. To demonstrate this, data are presented at a resolution of 10 × 10 × 10 µm across a field of view of 900 × 720 µm, corresponding to the 10× lens used in the experiment. To obtain this out-of-plane resolution with a correlation-based algorithm we would require a numerical aperture more typical of a 20× lens, with a correspondingly smaller field of view. The data agree with the CFD within the experimental uncertainties and it is proposed that the method could be important even in flows where only the in-plane velocity components are of interest. With the current system, a single measurement can determine the in-plane velocity field throughout a 900 × 720 × 45 µm volume, large enough to cover a significant section of a micro-device. The out-of-plane resolution is limited only by the number of images taken and, ultimately, the size of the particles.