In line with Article 20 (9) of the Tobacco Products Directive (TPD) 2014/40/EU, a guidance document outlining a reporting system of suspected adverse effects from electronic cigarettes and their refill liquids was produced by Work Package 4 entitled ‘Integration into national policies and sustainability’ of the Joint Action on Tobacco Control (JATC). The JATC was a European project that lasted three years (2017–2020), with the general objective of providing support for the implementation of the TPD throughout the 27 European Union Member States (EU MS). The reporting system described in the guidance document includes a short reporting template for the reporting of adverse effects on human health from electronic cigarettes and refill liquids, both by Economic Operators (EO) and by National Competent Authorities (NCA). The present guidance document aims at providing the necessary steps and modalities that each MS should follow if involved in the development of a system for the reporting of suspected adverse effects on human health from electronic cigarettes and refill liquids.