Confocal Micro-Particle Tracking (CM-PT) is used to capture 3-D velocity profiles of unsteady fluid flow in microchannels. Traditionally, low temporal resolution has limited the use of confocal microscopy in applications where high-speed imaging is necessary, such as dynamic flow systems. However, recent advances in spinning disk and camera technology have increased the temporal resolution to 1000 frames per second. Confocal microscopy captures thin planes of data that are used to produce high-resolution images with increased signal to noise ratio over widefield microscopy techniques. By combining the high-speed thin optical slicing ability of the confocal microscope with a continuously driven piezo objective controller it is possible to measure 3-D velocity profiles for unsteady flows. Quickly scanning through the depth of the channel with the objective controller allows imaging of 40 volumes per second for a 25-micron deep channel. This powerful technique provides a non-intrusive method for characterizing many important flow systems, such as in-vitro studies of pulsing blood flow within the micro capillaries.