Fungi causing apple storage rots in the Lower Elbe region were examined for resistance against the methyl benzimidazole carbamate (MBC) fungicide thiophanate-methyl. In Neofabraea perennans, the most important post-harvest pathogen, strains with sensitivity (EC50 = 0.07 ppm), intermediate resistance (EC50 = 1.0–3.4 ppm) or high resistance (EC50 > 400 ppm) were found. A similar pattern was observed for N. alba in the Lower Elbe region, and for additional isolates of both species collected from the East German state of Brandenburg. In contrast, Neonectria galligena showed a uniform response of intermediate resistance to thiophanate-methyl (EC50 = 1.0–1.7 ppm). Glomerella acutata isolates were partially inhibited by low fungicide concentrations (EC50 = 0.2–0.6 ppm) but showed residual (20–40%) mycelial growth even at 400 ppm. Since Neofabraea strains with intermediate and high resistance were distributed throughout the Lower Elbe region, pre-harvest applications of thiophanate- methyl against storage rots cannot be recommended at present for this important centre of German apple production.