Background: Celiac disease (CD) is defined as a systemic autoimmune disorder induced by gluten and other prolamins, which leads to gradual histopathological damage of the duodenum mucosa, intestinal villous atrophy, in particular. The brush border of enterocytes produces disaccharidases, including lactase. Lactase deficiency may be primary - genetically determined or secondary- due to damage to the intestinal villi. To exclude the primary cause of lactase deficiency, LCT gene polymorphism is necessary to evaluate. Objective: In patients diagnosed with CD, the intestinal villi should recover after strict adherence to the gluten-free diet, and therefore no lactase enzyme deficiency secondary to the underlying disease should be observed. Methods: The study group consisted of 38 patients, 30 women and 8 men (Group 1), who presented symptoms suggesting CD at the time of diagnosis, histology of duodenal mucosa samples revealed Marsh grade 3 and had confirmed the presence of HLA-DQ2 or DQ8 genes and had the gluten-free diet recommended. The control group consisted of 31 healthy volunteers, 18 women and 13 men. A hydrogen breath test (HBT) was performed in all groups with 50 g of lactose dissolved in 250 ml of water. Among patients with a positive HBT in all groups, a blood sample was collected to determine the C/T (-13910) and G/A (-22018) polymorphism in the promoter of the LCT gene responsible for the synthesis of the lactase enzyme. Among patients with lactase deficiency confirmed in HBT, LCT gene analysis was performed by assessing the C/T (-13910) and G/A (-22018) polymorphisms.Results: A significantly higher incidence of lactase enzyme deficiency was found in Group 1 (n=27, 71.1%) compared to the control group (n=10, 32.3%) (p<0.01). Severe lactase deficiency was observed more frequently in the group 1 than in the control group (n=19 (50%) vs. n=5 (16.1%); p<0.01), while mild and moderate lactase enzyme deficiency was observed with similar prevalence. Severe deficiency of the lactase enzyme was found significantly more frequently in the group of patient who did not strictly follow the diet than in the group declaring a strict adherence to a gluten-free diet (n=13 (65%) vs. n=6 (33%); p<0.05). No significant difference was found in the frequency of the C/T (-13910) and G/A (-22018) polymorphism in the promoter of the LCT between the analyzed groups with previously positive HBT test. Only in group 1, in 5 (18.5%) patients presence of LCT gene variants responsible for lactase enzyme deficiency was not detected. Conclusions: Among patients with CD, lactase deficiency was confirmed in the majority of the study participants, of whom only about half had primary lactase deficiency. In the study group, a correlation was demonstrated between severe deficiency of the lactase enzyme and non-adherence to gluten- free diet.