Pattern formation in Drosophila embryogenesis has been widely investigated as a developmental and evolutionary model of robustness. To ask whether genetic variation for pattern formation is suppressed in this system, artificial selection for divergent egg size was used to challenge the scaling of even-skipped (eve) pattern formation in mitotic cycle 14 (stage 5) embryos of Drosophila melanogaster. Three-dimensional confocal imaging revealed shifts in the allometry of eve pair-rule stripes along both anterior–posterior (A–P) and dorsoventral (D–V) axes as a correlated response to egg size selection, indicating the availability of genetic variation for this buffered trait. Environmental perturbation was not required for the manifestation of this variation. The number of nuclei at the cellular blastoderm stage also changed in response to selection, with large-egg selected lines having more than 1000 additional nuclei relative to small-egg lines. This increase in nuclear number in larger eggs does not scale with egg size, however, as nuclear density is inversely correlated with egg length. Nuclear density varies along the A–P axis but does not correlate with the shift in eve stripe allometry between the selection treatments. Despite its macroevolutionary conservation, both eve stripe patterning and blastoderm cell number vary genetically both within and between closely related species.