The molecular networks that pattern leaf complexity, lobes, and serrations, have been studied in detail. Our understanding of the genetic underpinnings of leaf thickness, a highly functional quantitative trait, however, is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a near-isogenic line (IL) population derived from the desert tomato species Solanum pennellii, and identified quantitative trait loci (QTL). Significant correlations of leaf thickness with a suite of traits suggest that thickness is patterned in concert with other aspects of leaf morphology. Thicker tomato leaves have dramatically elongated palisade parenchyma cells - a common feature of many thick leaves. To dissect the molecular networks that pattern thickness during leaf development we inferred Dynamic Bayesian Networks of gene expression across early leaf ontogeny (plastochron stages P1-P4) in two ILs with thicker leaves. We identified regulators of S. pennellii-like leaf shape and present molecular evidence for alterations in the relative pace of the cellular events underlying leaf development, which may lead to the patterning of thicker leaves. Collectively, these data suggest genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato.