Monitoring systems based on traps with female attractants are expected to enhance forecasting of insect population size and damage. The optimal placement of such traps should match the small-scale distribution of ovipositing females. In the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), fruit infestation takes place in proximity to the oviposition site. We characterized the within-tree distribution of codling moth infestations and the size of uninfested fruit based on a survey of 40,000 apples (Malus spp.) from trees belonging to 160 different apple genotypes and growing in two different environments. Each tree was subdivided into 12 sectors, considering canopy aspect (north, east, south, and west) and canopy height (bottom, middle, and top). This study revealed that fruit infestation by the first but not by the second generation of larvae correlated significantly with canopy aspect. Similarly, fruit size differed significantly between the north- and the south-facing tree side for the period of infestation by the first but not by the second larval generation. Significantly lower fruit infestation was observed on the north- compared with the south- or east-facing tree side for the first generation. A significant influence of canopy height on larval infestation was observed in three of eight assessments, in which the middle height level showed the highest infestations. Significant differences in within-tree distribution of codling moth infestation suggest that oviposition preference is guided by nonrandom factors including microclimate, fruit phenology, and wind direction. These cultivar-independent findings should be considered in future monitoring systems that focus on female codling moth.