Debug controls for debugging a distributed application are included in messages that are also used by the distributed application to transport data. A debug initiator causes debug controls to be inserted in the header portion of a message that is being transported across a distributed system. The debug initiator may insert debug controls directly or may cause a message router that receives the message to merge debug controls into the message. The message router may receive debug controls from the debug initiator or from configuration files that are maintained at the message router. The message, which now includes distributed application data and debug controls, is routed to a message recipient. The message recipient accesses the message to identify debug functions that are to be performed at the message recipient. The message recipient performs at least one of the identified debug functions.