Based on the number of questions about apples received at the Plant Clinic, there are many home gardeners in Illinois growing apple trees. Fruit pathology specialists recommend pruning apple trees as soon as the crop is off. It is probably a little better for tree health to prune in March, but it is much easier to do a good job in the fall when healthy plant material is easy to distinguish from diseased tissue.
The goal of pruning is to remove all the dead tissue. This practice limits the development of fire blight, black rot, sooty blotch, fly speck, and apple scab. If the tree is known to be infected with fire blight, be sure to disinfect the pruners after every cut to prevent further spread of the disease. Disinfect by dipping the blades in 10 percent Clorox or rubbing alcohol solution.