Fire blight is the most important bacterial disease in apple (Malus × domestica). Owing to the severity of the caused damages, fire blight resistance is an important breeding objective. In the past, various phenotypic screening methods and strategies have been used to identify new sources of fire blight resistance for breeding. In this study, breeding material, modern cultivars and heirloom accessions were phenotyped by artificial inoculation of shoots under greenhouse (n=273) and flowers under field conditions (n=20) and genotyped for known resistance genes and quantitative trait loci by using molecular markers. A comparison between the two phenotyping methods was made in relation to the two control varieties ‘Gala Galaxy’ and ‘Enterprise’. The results obtained for the resistance sources FB_MR5, Fb_E and FB_F7 are consistent with previously published data, showing a large effect of the two major resistance genes FB_MR5 (‘Malus × robusta 5’) and Fb_E (‘Evereste’). Genotypes carrying FB_F7 showed greater variation in their resistance levels, but were on average less susceptible than ‘Gala Galaxy’ and genotypes with no known resistance gene or quantitative trait locus (QTLs) in both tests. No correlation was found between the results of 18 genotypes phenotyped with both inoculation methods. The ranking of genotypes according to their flower and shoot fire blight resistance varied between the two methods. However, 11 of the 18 tested genotypes showed no significant difference between the results of the two methods. Additionally, it was found that flower shedding appears to be an important triggered mechanism for flower resistance to fire blight.