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Are second level audits for FP7 only targeted to projects or can they also be related to a whole organisation, having several EU-projects?

Answer: 

In FP7 the Commission usually audits 3 projects at a partner's place at once (for large organisations). A Commission' audit is always based on the organisational rules and the systems used in EU-projects. However, the EU COM audit unit has the power and the possibility to involve all other EU projects when they find a logical / consistent error that seems to be “systematic”. Then an extrapolation of the audit findings on all other projects is possible and all other projects may be recalculated.