Chilling injury (CI) is a major physiological problem limiting consumption and export of peach and nectarine (Prunus persica (L.) Batsch). To clarify the genetic basis for chilling injury, inheritance of the major CI symptoms mealiness, flesh browning, flesh bleeding, and flesh leatheriness were examined over three years in two related peach progenies. In addition, genetic relationships among traits and the year-to-year variation in trait performance in these progenies were tracked. Both populations also segregated for Freestone-Melting flesh (F-M) and yellow flesh. There were significant differences in CI symptoms among years. The major gene endoPG, which controls the F-M locus, provides resistance to mealiness in nonmelting flesh fruit. Only fruit with melting flesh can develop mealiness if the tree possesses other genetic susceptibility factors and/or experiences inducing conditions. The F-M locus also greatly influences susceptibility to flesh bleeding, although the physiological mechanism for this disorder is unclear and may be controlled by a different gene closely linked to endoPG. Unlike mealiness, flesh bleeding occurred primarily in non-melting flesh fruit, particularly when the fruit is white-fleshed. Flesh browning incidence was greater in mealy fruit and was not associated with flesh bleeding. Breeding for CI resistance is thus a viable long-term strategy to reduce losses in the fresh and processed peach and nectarine industries. This study is an important first step to understanding genetic control of CI symptoms in peach.