The organisational process flow can be defined as the series of operations which lead from an input (data, raw materials, products) to an output (piece of information, product or service). In this way, the processes can include various sequences of tasks. Today, needs in organisational analysis tend to be approach based on processes in order to satisfy the needs of new management tools. Among these we can find ABC method, construction of Balanced Scorecards, ERP or ISO 9000 standard. For our study we shall retain the last two tools because the process analysis, which is associated to them, has a particularly important impact on organisation while ABC method and construction of Balanced Scorecards use this type of analysis only to describe the existing and measure its performance. ERP and ISO 9000 standard generate issues about organisational flows. These two management tools indeed require an analysis in terms of process flow for two reasons :-to allow the implementation of the management tool-and to reduce the risk of failure of this application due to the lack of relevant analysis of the concerned organisation and of its specificities. In such conditions, we can ask ourselves what is the contribution of the organisational representation based on processes in an approach of organisational clarification and integration. It is indeed a question of clarifying the organisation in order to know how to set up management tools in an effective way (ERP or ISO 9000 standard in our empirical case) and simultaneously, to favour the organisational integration in order to facilitate the objective of control linked to these tools. Thus, the concept of organisational integration is translated here by the will to integrate every element of the organisation in a system of generalised control (indeed, these two management tools try to cover the whole organisation). Our analysis is therefore linked to the wider problem of the organisational control theory. We will first perform a theoretical analysis of the expected outcome linked to the realisation of a process analysis within the organisation. This theoretical analysis will be based on the hypothesis of reducing the organisational complexity as well as on the hypothesis of cartesian method. The second hypothesis supposes that we understand better an organisational activity by choosing an analytical approach. This will be followed by the demonstration that the process analysis is an essential step in implementing an ERP and in obtaining the ISO 9000 certification for an organisation. Finally, we will show the organisational consequences observed empirically in six case studies following to the process analysis. Hence, the assumption of a better clarification and integration of the organisation is confirmed for both ERP and ISO 9000 management tools. However, we observe a coercion dimension for the ERP and learning dimension for the ISO 9000. Indeed, while the process analysis is presented as an intermediate step to the implementation of an ERP, it is, for the ISO 9000 standard, not an obligatory step, but the result of the implementation of the standard. The process map, which follows, is a fundamental tool of the quality management system. Thus, the process analysis is for ERP only a preparation for the computer integration and data processing for the organisation (a means), while for ISO 9000 it is one management tool of the organisational risks, i.e., an instrument preventing the dysfunctions (an end). Another difference between the process analysis linked to the implementation of an ERP or of the ISO 9000 standard, is linked to the pursued objectives. While in the first case, it is a matter of adapting the organisation to the ERP, in the second case, the purpose is to make the organisation transparent and to give it the capacity to improve itself. We are, in the first case, in an instrumental approach of the processes analysis and in the second, in a more constructivist approach Finally, it is important to remember the high cost of implementation of ERP and ISO 9000 better clarification and for an integration of the organisation can be pursued through the process analysis which precedes the implementation of these two tools, it is important to increase the chances of success by directing the process analysis to a learning approach rather than to a coercion approach. This is also the occasion to see once again that the rigidity of the model raises problem for the respect of the identity of the organisation represented as a set of workflows. The rigidity can, in different cases, destroy the organisation or, on the contrary, allows its evolution in a balance between the organisation and the process model.