A method, system and computer-readable storage for breakpoint management and reconciliation for business integration language specified programs is disclosed. The system includes a business integration language development environment including BPEL development environment cooperatively coupled to a BPEL engine; debug tooling accessible through the environment; and breakpoint management and reconciliation processor coupled to the debug tooling. The debug tooling comprises script display for displaying textual portions of script embedded in source code of a business integration language specified program, and at least one other display selected from a graphical process flow display, a debug display and a breakpoint module display. The breakpoint management and reconciliation processor manages establishing of symbolic breakpoints in the source code and reconciling corresponding breakpoints in an operable form of the source code. The script module display visually demarcates a location in the source code on reconciling its corresponding breakpoint to an encountered breakpoint.