One of the major issues in the monitoring and control of manufacturing systems is to determine how to effectively deal with unexpected disruptions (e.g. material unavailability, resource failures, unavail- ability of operators, rush orders, etc.). Existing approaches and tools offer few concepts that are specific enough and sufficiently generic to help in handling a broad variety of such unexpected events. The biological immune system potentially offers interesting features to face the threats (bacteria, viruses, cancers, etc.) that may harm an organism. This research aims to investigate this potential for the monitoring and control of manufacturing systems at the occurrence of disruptions. Based on analogies that we point out, we suggest a framework to help with the design of software tools that are more able to assist decision makers in dealing with various types of disruptions occurring in a manufacturing system. A first prototype implementation, developed using a multi agent approach, contributes to show the feasibility and the interest of this immune based framework