Objective: To investigate the differential expression of the thymic stromal lymphopoietin isoforms, short and long, and discern their biological implications under eosinophilic gastroenteritis. Methods: The expression of thymic stromal lymphopoietin and its two isoforms in tissues was assessed by quantitative RT-PCR in healthy controls (n = 24) and patients with eosinophilic gastroenteritis (n = 17). Results: Thymic stromal lymphopoietin mRNA was significantly reduced in eosinophilic gastroenteritis when compared with healthy controls (p < 0.0001). A significantly lower amount of short thymic stromal lymphopoietin mRNA was observed in eosinophilic gastroenteritis when compared with controls (p < 0.05), while a significantly higher amount of long thymic stromal lymphopoietin mRNA was observed in eosinophilic gastroenteritis when compared with controls (p < 0.05). Peak eosinophilic count is significantly positively correlated with the expression of long thymic stromal lymphopoietin mRNA in the gastrointestinal mucosal of patients with eosinophilic gastroenteritis (r s = 0.623, p < 0.005), while peak eosinophilic count is significantly negatively correlated with the expression of short thymic stromal lymphopoietin mRNA in the gastrointestinal mucosal of patients with eosinophilic gastroenteritis (r s = −0.4474, p < 0.05). Conclusions: Abnormal mucosal thymic stromal lymphopoietin expression may contribute to gastrointestinal mucosa damage in eosinophilic gastroenteritis.