This publication presents the core European protocol for a series of proposed influenza vaccine effectiveness studies. The protocol includes a proposed plan for pooled analysis and has recently been adapted to measure vaccine effectiveness for the pandemic vaccine in 2009-10. Together with its twin publication ‘Protocols for cohort database studies to measure influenza vaccine effectiveness in the EU and EEA Member States’, this publication covers all methodological issues in the design and implementation of vaccine effectiveness studies, both for seasonal and the new A(H1N1)v influenza.