A method, system and apparatus for applying virtual threads in debugging a business process program. In accordance with the present invention, different activities in a business process can be associated with corresponding virtual thread identifiers where groups of the activities related to one another through corresponding links can be assigned a single virtual thread identifier. Based upon the association of activities with corresponding virtual thread identifiers, a directed graph of different activities of different virtual thread identifiers can be generated. Accordingly, debug operations including applying breakpoints, step over debugging and the like can be applied to a business process program regardless of the host platform for any one activity in the business process program.