We prove that the conjugacy problem in right-angled Artin groups (RAAGs), as well as in a large and natural class of subgroups of RAAGs, can be solved in linear-time. This class of subgroups contains, for instance, all graph braid groups (i.e. fundam
ental groups of configuration spaces of points in graphs), many hyperbolic groups, and it coincides with the class of fundamental groups of ``special cube complexes studied independently by Haglund and Wise.
