Techniques for reliable binary instrumentation based on annotation information are described. A binary file that comprises a code section representing the executable code of a computer program is accessed. The binary file also comprises annotation information that indicates the boundaries of one or more portions of the computer program. Accurate data flow information and control flow information may be generated based on the annotation information included in the binary file. The binary file is instrumented by inserting a set of instrumentation code at one or more points in the code section of the computer program. The one or more points are determined based on the data flow information and the control flow information.