Existing work on the verification of information flow in threads mainly focuses on timing channels. However, this paper shows that system calls, such as‘fork’ or ‘join’ with side effects, can also be used to create covert channels intentionally or accidentally. The study results in a dependency logic for verifying information flow in multi-threaded programs where improper calls over thread controlling primitives with side effects could incur illegal information flow. The logic can express the data flow, control flow and the side effects of thread-controlling system calls, and can reason about the dependency relationship among variables and thread identities, to determine whether secret variables interfere with public ones in multi-threaded programs.