The aim of this study was to assess the frequency of the occurrence of lactose intolerance in children with an IgE-dependent allergy to cow's milk. The study group consisted of 48 children diagnosed with IgE-dependent allergy to cow's milk proteins (group I). The control group (group II) included 40 children, in a similar age range and with normal architecture of the mucosa of the small intestine, with excluded food allergy. All patients underwent gastroduodenoscopy with biopsy, in which the activity of lactase was determined. The average activities of lactase in the group of patients with allergy were lower than in group II and amounted to 5.6 and 8.64 U/1 g. Lactase deficiency was observed in 6/48 patients in the group of patients with allergy. In group II, lactase deficiency was observed in 20%, which corresponds to the frequency of lactase intolerance in Poland. Lower activity of lactase was statistically significantly more common in older children. A reduced activity of lactase was more frequent in children with atrophy of the intestinal villi; however, that difference was not statistically significant. Lactose intolerance was less frequent in children with a diagnosed IgE-dependent milk proteins allergy. Due to the positive role of lactose in the diet, it seems that including a lactose-free formula in patients with diagnosed IgE-dependent allergy to milk is not necessary.