Code can be injected into a compiled application through the use of probes comprised of instrumentation code. Probes can be implemented in a custom high level language that hides low level instruction details. A directive file contains instructions on injecting a probe into a compiled application. An instrumentation engine reads these instructions and injects the probe into the compiled application at the appropriate injection points. Multiple probes can be used, and can be stored in a probe library. Each probe can inject code into the application at, for example, a package, class, method, or line of the compiled application. Calls can also be made to external runtime libraries.