A debugger that includes a breakpoint protection mechanism that detects when the program being debugged has been modified to overwrite one or more instructions corresponding to existing breakpoints. When the debugger halts execution of a program being debugged, all of the set breakpoints are checked by determining whether the instruction corresponding to each breakpoint has changed. If any of the instructions corresponding to the breakpoints has changed, the corresponding breakpoint is removed. An optional warning may be provided to the user to inform the user of any removed breakpoints.