A popular technique for growing smaller cherry trees is to select a tree with a dwarfing rootstock. Rootstocks such as Mazzard, Mahaleb, Gisele or F12/1 all trigger compact growth and excellent performance in poor soils. While a few cherry trees have been bred for small size, you can generally expect a more disease-resistant tree by grafting a hardy cultivar to an equally hardy rootstock. Besides the general resistance to disease, factor in the rootstock's resistance to fruit splitting or cracking and its overall suitability for your local climate. For example, the F12/1 is very vigorous and has excellent resistance to canker and pseudonomas, a common bacterial problem among cherry trees. On the other hand, its roots are prone to crown gall, another bacterial disease.
The few true dwarf cherry trees in existence are fairly resistant to disease. The Compact Stella is one of the only dwarf self-pollinators. The cultivar is also less subject to cracking fruit than most cherry trees and generally less susceptible to common diseases than the most popular cultivars, such as Bing. But it is only cold-hardy to climates with annual lows of around minus 10 to minus 15 degrees Fahrenheit. Starkrimson is also compact and disease-resistant. It's more cold-hardy than Compact Stella and has particularly high yields with notably large and sweet fruit. If you prefer a sour cherry tree, North Star is a self-pollinating dwarf that's generally disease-resistant.
Selecting a dwarfing rootstock or a genetic dwarf that's generally vigorous to disease is a first step to ensuring your cherry tree's health. As in the case of the F12/1 rootstock, however, most cultivars are more resistant to one issue and less resistant to another. To determine the best tree for your area, consult with your local horticultural extension about the most common diseases and pests in your area. Brown rot and cherry leaf spot are among the major diseases affecting cherry trees. While not strictly speaking a disease, fruit cracking or splitting is another pitfall of less resilient cultivars. Major pests affecting cherry trees include the cherry fruit fly, black cherry aphid, cherry slug and the fruit tree leaf roller.
As when planting any variety of tree, it's vital to select a specimen well-suited to your growing zone. In general, tart cherry trees thrive in U.S. Department of Agriculture hardiness zones 4 to 6 and sweet cherries grow best in zones 5 through 7. You can further support the tree's health by planting the tree in a well-drained area, one of the major causes of brown rot. Avoid setting the tree too deeply in the ground, another potential cause for rot.