Dislocations in an HVPE-grown GaN substrate have been characterized by photoluminescence (PL) imaging, cathodoluminescence (CL) mapping and etch pit method. Most of the dislocations can be revealed in all three characterizations, while some of the dislocations are invisible in CL, but visible in PL and have corresponding etch pits. The different appearance of dislocations in PL and CL are discussed in terms of the difference in imaging and mapping (scanning), and the difference in excitation power density between PL and CL. In addition, TEM observation has been performed to help understand the dislocation structure of CL-invisible dislocations. The results have shown that one of the CL-inactive dislocations (TD-A) has a Burgers vector of only a-component, and its dislocation line has an 11 degrees tilting angle towards [-1100], and a 15 degrees tilting angle towards [-1-120], with respect to the c-axis. In comparison, another CL-visible dislocation nearby (TD-B) also has only a-component of Burgers vector, but the line direction is different to TD-A. The results have suggested that electrical properties of dislocations in GaN are not only determined by the Burgers vectors but also strongly depend on the direction of dislocation line.