Background: Bottle-fed infants sometimes develop intestinal cow’s milk allergy (ICMA). Because cow’s milk-specific IgE antibody (CM-IgE) levels are normal, the lymphocyte stimulation test (LST) has been proposed as an alternative diagnostic test for ICMA. The present study evaluated the diagnostic value of LST in a large number of patients with ICMA in Japan. Methods: Ninety-six infants who developed intestinal symptoms after ingestion of cow’s milk formula and showed remission of symptoms after elimination of this food were enrolled as patients with probable ICMA. Seventy-two subjects with normal CM-IgE levels and a positive result in an oral food challenge test (OFCT) for cow’s milk formula were diagnosed with ICMA. Another 10 infants with normal CM-IgE levels and a negative OFCT result were diagnosed with nonspecific intestinal symptoms (NIS). The status of cell-mediated immunity against cow’s milk proteins was estimated by LST for ĸ-casein. Results: In the 72 patients with ICMA (38 boys and 34 girls), the median age at onset was 9 days. Sixty-two of 72 (86.1%) patients with ICMA tested positive in the LST for ĸ-casein. In contrast, only 2 of the 10 NIS infants tested positive. The incidence of a positive LST result was significantly higher in the ICMA group than in the NIS group (p < 0.0001). The area under the receiver-operating characteristic curve for this test was as high as 0.856. Conclusions: This study strongly suggests that the LST for ĸ-casein is a useful diagnostic test for ICMA.