System aware performance counters including a processor for performing a method that includes executing a predefined code segment of an application, the executing on a processor. The executing includes executing an instrumented thread included in the predefined code segment. The method includes performing a first action associated with executing the instrumented thread in the predefined code segment, and registering the instrumented thread. A performance counter associated with the predefined code segment is started. Also, the execution of the predefined code segment is paused and the performance counter is paused. The method further includes performing a second action associated with pausing the executing of the predefined code segment. The executing of the predefined code segment is resumed and the performance counter is resumed responsive to resuming the executing of the predefined code segment. Also, a third action associated with resuming executing the predefined code segment is performed.