A method, system and apparatus for breakpoint management and reconciliation for business integration language specified programs. The system includes a business integration language development environment; debug tooling accessible through the environment; and, breakpoint management and reconciliation logic coupled to the debug tooling. The business integration language development environment includes a BPEL development environment cooperatively coupled to a BPEL engine. The debug tooling includes a script display for displaying textual portions of an embedded script; and, at least one other display selected from the group consisting of a graphical process flow display, a debug module display and a breakpoint module display.