A 3D particle-tracking velocimetry (PTV) algorithm is applied to the wake flow behind a heated cylinder. The method is tested in advance with respect to its accuracy and performance. In the accuracy tests, its capability to locate particles in 3D space is tested. It appears that the algorithm can determine the particle position with an accuracy of less than 0.5 camera pixels, equivalent to 0.3 mm in the present test situation. The performance tests show that for particles located in a 2D plane, the algorithm can track the particles with a vector yield reaching 100%, which means that a velocity vector can be determined for almost all particles detected. The calculated velocity vectors for this situation have a standard deviation of less than 1%. The performance is also tested on a mixed convection flow behind a heated cylinder in which the 2D flow transits into a 3D flow. As there is no exact solution of such a flow available, the 3D PTV results are compared with visualisation results. The results show that the 3D PTV method can capture the main features of the 3D transition of the 2D vortex street.