Abstract Early life adversity (ELA) is a risk factor for later life emergence of functional and inflammatory GI disorders in people and animals. In this study, we compared the early GI immune responses in male piglets exposed to early weaning (EW) at 16–18 d of age, a form of ELA we’ve previously shown result in altered GI developmental and health trajectories similar to ELA in humans, with that of late weaned piglets (LW: 28 d of wean age). RNA transcriptome analysis of ileal mucosa at 24h post-weaning revealed that EW pigs exhibited a greater number of differentially expressed genes (765 vs 110 genes, for EW and LW piglets, respectively), characterized by a large number of upregulated genes associated with immune cell trafficking and inflammation. Mast cells (MC), stress-sensitive innate immune cells which orchestrate the immune response, were acutely activated in EW and LW pigs but in a differential manner. Compared with LW piglets, EW piglets exhibited higher levels of serum histamine which coincided with a downregulation in the gene expression of histamine degrading enzymes, DAO and HNMT in intestinal mucosa. Mast cell tryptase (MCT7) and chymase (CMA1) gene expression were upregulated in ileal and colonic mucosa (within 3h post-weaning) in both EW and LW piglets; however, this response was greater in LW pigs. Together, these data show that weaning stress in piglets induces rapid GI MC activation which precedes immune cell recruitment and intestinal inflammation and that postnatal age has a significant influence on the level and nature of this response. Further investigation of how EW and LW piglets differentially regulate early GI immune responses is expected to provide new insight into the mechanisms of GI and immune disorders associated with ELA.