Atopic dermatitis (AD) is a chronic inflammatory skin disease. Skin and gut are the organs that first encounter antigens and environmental triggers. The mechanisms behind the relation between skin and gut immune responses in AD have not been identified yet. To investigate mucosa-associated epithelial chemokine (MEC/CCL28), thymus-expressed chemokine (TECK/CCL25), periostin and zonulin levels in infants with AD. Children under one year old participated in the study. We used a propensity matching score. We included 39 infants who had active AD lesions at the time of evaluation. Serum MEC/CCL28, TECK/CCL25, periostin and zonulin levels were measured. We examined age and sex matched 39 infants with AD and 39 healthy infants. Median value of zonulin was lower in infants with AD [49.2 (27.1-71.8) ng/mL] compared to healthy controls [58.5 (27.3-80.8) ng/mL] (P < 0.001). Infants with zonulin levels ≤55.15 ng/mL had 11.64 times more risk of developing AD than the infants with zonulin levels >55.15 ng/mL. Infants whose MEC/CCL28 levels were ≥8.3 ng/mL had 5.83 times more risk of developing AD than the infants with MEC levels <8.3 ng/mL. Duration of AD and SCORAD index score did not show correlation with MEC/CCL28, TECK/CCL25, periostin and zonulin levels. Low zonulin levels and high MEC/CCL28 levels in infants may show an increased association with AD.