Joule heating (JH) is a ubiquitous phenomenon in electrokinetic microfluidic devices. Its effects on fluid and ionic species transport in capillary and microchip electrophoresis have been well studied. However, JH effects on the electrokinetic motion of microparticles in microchannels have been nearly unexplored in the literature. This paper presents an experimental investigation of JH effects on electrokinetic particle transport and manipulation in constriction microchannels under both pure dc and dc-biased ac electric fields. It is found that the JH effects reduce the dielectrophoretic focusing and trapping of particles, especially significant when dc-biased ac electric fields are used. These results are expected to provide a useful guidance for future designs of electrokinetic particle handling microdevices that will avoid JH effects or take advantage of them.