Abstract The results of Slovenian surveillance system of AEFI which was in place for the early detection and investigation of rare adverse events were analysed. The reports about AEFI obtained from physicians, and self-assessment questionnaires from vaccinated persons showed predominantly non-serious and expected side effects. Nine reports (3%) included serious AEFI. No deaths consequent to vaccination were reported. A total of 1170 AEFI were reported by physicians and 1030 by self-assessment. Overall, the most commonly reported AEFI either by physicians or persons were local site reactions (37.3% and 50.5%), tiredness (11.9% and 6.8%) and fever or malaise (10.8% and 6.3%). More than 100,000 people were vaccinated with pandemic vaccines in Slovenia. The type and the frequency of AEFI detected through Slovenian AEFI surveillance system are comparable to the results from other surveillance systems. The benefit-risk balance for the pandemic vaccines used in Slovenia remains positive.