Abstract Background Early diagnosis of tuberculosis remains challenging due to the nonspecific clinical manifestations that can mimic other gastrointestinal diseases and range from acute to chronic abdominal disease. In recent decades, latent tuberculosis (LTI) has been of particular interest. Patients with inflammatory bowel disease (IBD) are at risk of contracting tuberculosis. Aim to identify the incidence of LTI in patients with IBD and its effect on the clinical, laboratory, endoscopic and morphological activity of IBD. Methods The study included 350 patients with IBD, who were monitored and a group of patients (188 people (UC = 80, CD = 101, MC = 7) who did not respond / or poorly respond to basic IBD therapy were identified. In this group, the determination of the quantiferon test was carried out. To achieve this goal, two main hypotheses were considered: assessment of IBD-associated and systemic vascular lesions (h/s CRP, platelet count, homocysteine, vit D, urine albumin, fecal calprotectin and lactoferrin; α-TNF, IL-1,IL-2,IL-4,IL-6,IL-8,IL-10,IL-18; endoscopic examination with pathomorphological assessment), assessment of changes in the thickness of the vascular intima and blood flow velocity (based on the doppler determination of the pulse wave velocity (PWV) and the thickness of the intima media (CIMT) on the common carotid, vertebral and subclavian arteries). Results The number of positive responses to the quantiferon test was found in 37 patients (19.7%) / 10.6%) out of 188 patients (53.7%); positive skin tests (Mantoux reaction) ≥5 mm in 78 (22.3%) patients; altered peritoneal lymph nodes in 28 (8%), pulmonary and pleural TB in 9 (2.57%) patients. There were no patients with intestinal TB / “+” TB PCR in the gastrointestinal tract tissue. The prevalence of positive cases according to the quantiferon test was: in the general group of patients - 10.6%. Laboratory indicators for both IBD and systemic vascular lesions were higher in the group of patients with latent tuberculosis (Table 1, Table 2). Damage to the vascular bed (based on doppler determination of pulse wave velocity (PWV) and intimal thickness (CIMT) on the common carotid, vertebral and subclavian arteries) was more pronounced in the group of patients with latent tuberculosis (CIMT (mm) 0.68 ± 0, 1 / 0.67 ± 0.2; PWV (sm / s) 93.3 ± 2.2 / 97.2 ± 1.4). Conclusion Conclusion. Comparing the results of the data before and after the treatment of latent TB in patients with IBD, certain dependences of the influence of infection on the course of IBD (h/s CRP, platelet levels, homocysteine, fecal calprotetin and lactoferrin, IL-8 and a decreased vit. D; changes, associated with damage to the vascular bed), endoscopic and morphological activity.