Abstract A series of small-scale controlled inoculation experiments has been conducted during 2005–2009 to determine whether temperature and controlled atmosphere (CA) storage conditions affect significantly the incidence of Botrytis cinerea and Neonectria galligena rots of apples and to assess whether CA regimes can be ‘fine-tuned’ to suppress fungal rotting. The incidence of B. cinerea and N. galligena rots on apple was reduced consistently by storage in lower temperatures (1.5–2°C). In no case was the disease incidence significantly higher than that under air storage conditions. However, the effect of CA conditions on rot development varied greatly from year to year so that overall there were no significant effects of CA conditions on the incidence of rot during storage till the following April. Thus, we can neither fine-tune CA conditions to reduce rot development nor exploit the advantages of lower storage temperatures for Cox and Bramley for this purpose due to inevitable development of low temperature breakdown. Further research is needed to study the effects of ethylene control technologies and modulated storage temperatures on rot development.