Absence or long delay of budbreak, also known as prolonged dormancy, is the most important symptom during incomplete dormancy. Budbreak number was evaluated to quantify seedling response to chilling and selection on excised and intact 1-year-old apple (Malus ×domestica Borkh.) seedlings under controlled and natural environmental conditions. Indices based on: 1) the number and distribution of budbreak (prolonged dormancy grade = PDG); 2) the number of buds breaking, including shoot length with increased budbreak as part of the calculation (prolonged dormancy index = PDI); and 3) budbreak number per 100-cm shoot (NB) were tested in association with budbreak time (TB). The indices expressed the effects of cold treatments that induce earlier and higher numbers of budbreak. PDI and NB, but not PDG, identified families with increased budbreak. Seedlings with high PDG and NB were also associated with families in which high chill requiring parents were used, indicating that TB as pre-selection criterion may fail to identify seedlings with increased budbreak. Response to pre-selection for increased budbreak using PDG could be verified with the PDS and NB indices in seedlings and seedling clones. The NB of intact 1-year-old shoots under natural conditions is recommended as a pre-selection criterion against prolonged dormancy in suboptimal winter conditions.