This report contains a guide and a European harmonised protocol prepared within the framework of the Working Group 3 on source apportionment of the Forum for Air Quality Modelling in Europe (FAIRMODE). It has been initiated as a JRC initiative for the harmonisation of source apportionment with receptor models, in collaboration with FAIRMODE as well as with the European networks in the field of air quality measurements (AQUILA), and then further with the European COLOSSAL (Chemical On-Line cOmpoSition and Source Apportionment of fine aerosol) COST action. The JRC initiative also included a review of the methodologies used in Europe for source identification and intercomparison exercises for the quantitative assessment of the performance of source apportionment models. The document, drafted and then revised by a group of international experts, is organised following the logical sequence of steps to be carried out in a source apportionment study. Sections with increasing levels of complexity make it accessible to readers with different degrees of familiarity with this topic, from air quality managers to air pollution experts and modellers. It has been conceived as a reference document that includes tutorials, technical recommendations and check lists.