Variation in pesticide residues in space and time has not been investigated systematically in spite of the large variability found at single scales (e.g. between trees or orchards). Information on variability at different scales will support the development of sampling methods and more reliable prediction of residues. Experiments were conducted to quantify the spatiotemporal variability in initial spray deposit on apple leaves and fruit using a substitute tracer (zinc EDTA chelate). Five hierarchical spatial scales were defined as (1) between orchards, (2) between plots within an orchard, (3) between trees within a plot, (4) between zones within a tree and (5) between leaves/fruit within a zone. Similarly, two temporal scales were defined as (1) between applications within a single year and (2) between years. The initial zinc concentration was approximately log-normally distributed; the variability in initial deposit concentration was greater on leaves than on fruit. The average initial zinc deposition was significantly greater in the top and outside zones than in the middle zones within individual trees. The most important scale for driving residue variability is the within-zone unit-to-unit variation, contributing to 71 and 49% of the observed variability for leaf and fruit samples respectively. Variability at other scales was related to the variation in the tree architecture. The results indicated that stratified sampling on the basis of within-tree zone structures, with the effort focused on within-zone sampling, should be used for the determination of pesticide residues.