The European Commission requested the EFSA Panel on Plant Health to evaluate the likelihood of pest freedom at entry in the EU, including both regulated and non-regulated pests, potentially associated with unrooted cuttings of the genera Petunia and Calibrachoa produced under physical isolation in Uganda. The relevance of any pest for this opinion was based on evidence collected according to specific criteria, following the methodology used for high-risk plants adapted for the specificity of this assessment. Twelve EU-regulated pests [Bemisia tabaci (non-European populations), cowpea mild mottle virus (CpMMV, Carlavirus vignae), potato leaf roll virus (PLRV, Polerovirus PLRV), potato spindle tuber viroid (PSTVd, Pospiviroid fusituberis), potato virus S (PVS, Carlavirus sigmasolani, non-EU isolates), potato virus × (PVX, Potexvirus ecspotati, non-EU isolates), Ralstonia solanacearum, Ralstonia pseudosolanacearum, Scirtothrips dorsalis, tomato leaf curl Uganda virus (ToLCUV), tomato spotted wilt virus (TSWV, Orthotospovirus tomatomaculae) and tomato yellow leaf curl virus (TYLCV, Begomovirus coheni)] and one non-regulated pest (Nipaecoccus viridis) were selected for further evaluation. For the selected pests, the risk mitigation measures implemented in Uganda and described in the technical dossier were evaluated taking into account the factors reducing their efficacy. For these pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest. The degree of pest freedom varies between the pests evaluated, with the contact-transmitted viroid and virus [potato spindle tuber viroid (PSTVd, P. fusituberis) and potato virus × (PVX, P. ecspotati, non-EU isolates)] being the pests most frequently expected on Petunia and Calibrachoa spp. imported unrooted cuttings. Expert knowledge elicitation indicated, with 95% certainty, that between 9916 and 10,000 per 10,000 Petunia and Calibrachoa spp. unrooted cuttings would be free from these pests.