A delayed and local gastrointestinal hypersensitivity to cow's milk (CM) protein is difficult to diagnose and there are limited data on this disorder. The aim of this study was to investigate local intestinal cytokine secretion in the upper small intestine in children with delayed-type cow's milk allergy (CMA). Duodenal biopsy samples from 31 children with delayed CMA, 14 with celiac disease (CD), and 14 healthy controls were studied for the spontaneous release of IFN-gamma, TNF-alpha, IL-2, IL-4, IL-5, and IL-10, measured by cytometric bead array, and of TGF-beta and IL-6 measured by ELISA. The children with delayed CMA secreted more IFN-gamma than the controls (p = 0.006) and the children with CD (p = 0.006). The children with CD secreted more IL-6 compared to the controls (p = 0.008) and the children with delayed CMA (p = 0.002). The children with delayed CMA who had continuously been exposed to CM secreted less TGF-beta than the children with delayed CMA who avoided CM (p = 0.050), and showed a tendency towards lower secretion compared to the controls (p = 0.078). Secretions of TNF-alpha, IL-2, IL-4, IL-5, and IL-10 were low in general; however, the children with delayed CMA who did not avoid CM secreted more IL-4 and IL-10 than the controls (p = 0.016, 0.059). In conclusion, the children with delayed CMA showed up-regulation of IFN-gamma. Interestingly, TGF-beta secretion was up-regulated in those children with delayed CMA who avoided CM suggesting recovery of regulation mechanisms.