Apple trees produce many more flower clusters than needed for a full crop, but natural early season flower and fruitlet abscission drastically reduce the final fruit number. Natural fruit abscission varies significantly year to year. There have been attempts to try to model apple fruit abscission in the past. However, due to the great complexity of a perennial crop system in a dynamic environment with significant plant manipulations, regulatory processes and controlling environmental variables have been difficult to elucidate. In 1995, a field trial was planted at the New York State Agricultural Experiment Station in Geneva, New York with 3 apple cultivars (‘Delicious’, ‘Gala’, and ‘McIntosh’). Beginning in 2000 and for 18 years thereafter, we recorded the natural whole-season fruit abscission of untreated trees that received no chemical or hand thinning. We also estimated early season patterns of carbohydrate supply-to-demand each year with a carbon balance model. These data were used to correlate tree carbon balance status and other environmental variables with natural fruit abscission responses. In general terms, natural set, defined as final fruit/flower cluster, of ‘Gala’ averaged ˜1 fruit for each flower cluster (fruit set = 0.9), whereas fewer fruits were set on ‘Delicious’ and ‘McIntosh’ (fruit set = 0.7 and 0.6, respectively). Fruit set of ‘Gala’ was less variable than of ‘Delicious’ or ‘McIntosh’, and there was a clear pattern for decreasing fruit set when the number of initial flower clusters per tree increased. Fruit weight was less dependent on fruit number for ‘Delicious’ and ‘McIntosh’ than for ‘Gala’. Multiple regression models indicated that number of flower clusters per tree and average carbohydrate balance between 0–60 degree days (DD) after bloom and 300–360 DD after bloom were the main significant variables that explained 60–80% of the variability in natural fruit set or final fruit number. For ‘Delicious’, temperatures of the previous fall also explained a significant amount of variation in final fruit set and final fruit number. For ‘Gala’, carbon balance from bloom to shortly after petal fall and when fruits were about 18 mm were the two main periods, which were more sensible to carbohydrate deficiency triggering fruit abscission. A later susceptible period was also observed for ‘McIntosh’, suggesting a larger thinning window for this cultivar.