Genetically modified organisms are subject to a risk assessment and regulatory approval before entering the European market. According to legislation (Directive 2001/18/EC, Regulation (EC) No 1829/2003 and Regulation (EU) No 503/2013) and the EFSA guidance documents on the risk assessment of food and feed from genetically modified (GM) plants and on the environmental risk assessment of GM plants, applicants need to perform a molecular characterisation of any DNA sequence inserted in the GM plant genome. When a GM plant is designed to produce one or more newly expressed proteins, an aspect of the risk assessment process is to characterise these proteins and to reliably determine their levels in the GM plant tissues. A number of methods to measure protein expression levels are used and several experimental factors within these methods are of critical importance in order to obtain reliable results. This explanatory note provides details on key methodological aspects for the determination of newly expressed protein levels that should be considered and reported by applicants in order to harmonise the information in GM plant applications submitted to EFSA.