ABSTRACT: Early nutritional environment affects development and long-term health. Our objective was to determine the effect of maternal high fat diet (HFD) during pregnancy and lactation on neonate`s duodenum histomorphology and proteome. Female mice were fed either a control diet (10% kcal fat; C) or a HFD (60% kcal fat) for four weeks, and bred. On postnatal day 2, litters were standardized to ten pups and half the pups were cross-fostered to dams fed on different diets, creating four treatment combinations: C-C (control), C-HF, HF-C, HF-HF. On postnatal day 12, pups` duodenum were excised and prepared for histology and LC-MS/MS analysis of proteome. Villi were significantly longer in duodenum of HF-HF pups compared to all other treatments. However, crypt cell proliferation rate was not different among treatments. Over 3000 proteins were detected, with 1054 commonly expressed across all groups. Between control and HF-HF, HF-C or C-HF, 812, 601 or 894 proteins were differentially expressed (Tukey adj-P <0.05), respectively. Functional analysis clustered proteins upregulated in HF-HF versus control in fat digestion and absorption, extracellular matrix, cell adhesion, immune response, oxidation-reduction processes, phagocytosis and transport categories. Proteins downregulated were classified as RNA splicing, translation, protein folding, endocytosis and transport. Thus the effect of nutritional environment on intestinal tract structure and function is manifested as early as postnatal day 12. In particular, exposure to maternal HFD during pregnancy and lactation changed fat digestion and absorption processes, increased extracellular matrix and focal adhesion proteins, and heightened innate and active immune response.