Although the interest in and production acreage of organic fruit and vegetables has grown in recent years, there are questions about the viability of perennial crops such as apple (Malus ×domestica) in an organic system in Kentucky because of the long, hot, and humid growing season. Thus, the objective of this project was to assess the severity of the challenges to organic apple production in Kentucky. A high-density, organic apple orchard was established in 2007 in the University of Kentucky Horticultural Research Farm in Lexington. The orchard of apple scab (Venturia inaequalis)–resistant ‘Redfree’, ‘Crimson Crisp’, and ‘Enterprise’ trees on ‘Budagovsky 9’ (B.9) rootstock, trained in a vertical axis system, was managed using organically certified techniques and materials for disease and insect control since its inception. Tree growth, tree and fruit injury from insect pests and diseases, and yield over the period 2011–13 were studied. Periodic, shallow cultivation kept the ground beneath the trees free of vegetation once the lower limbs were pulled up and away from the path of the equipment. Vole (Microtus sp.) damage was a continuing problem despite the use of trunk guards and cultivation to remove habitat around the trees. Total fruit yield ranged from 1.2 to 8.1 kg/tree across years and cultivars, with the marketable proportion of the total yield averaging 68% for Redfree and 43% for Crimson Crisp and Enterprise over the 3-year period. The unmarketable fruit exhibited a high incidence of plum curculio (Conotrachelus nenuphar) damage, with generally less damage from codling moth (Cydia pomonella) and sooty blotch (Glosodes pomigena)/flyspeck (Schizathyrium pomi). In addition, in two of the three seasons, ‘Crimson Crisp’ and ‘Enterprise’, which were harvested at later calendar dates then ‘Redfree’, had significant levels of powdery mildew (Podosphaera leucotricha) injury, ‘Enterprise’ had significantly greater bitter rot (Glomerella cingulata), and ‘Crimson Crisp’ showed fruit and foliar damage from cedar apple rust (Gymnosporangium juniperi-virginianae). Because ‘Redfree’ was the only cultivar with an acceptable marketable proportion of the fruit crop, the use of early ripening disease-resistant apple cultivars may have the greatest potential for successful organic apple production in Kentucky and the surrounding region.