Several evidence suggests that, in addition to the respiratory tract, also the gastrointestinal tract is a main site of severe acute respiratory syndrome CoronaVirus 2 (SARS‐CoV‐2) infection, as an example of a multi‐organ vascular damage, likely associated with poor prognosis. To assess mechanisms SARS‐CoV‐2 responsible of tissue infection and vascular injury, correlating with thrombotic damage, specimens of the digestive tract positive for SARS‐CoV‐2 nucleocapsid protein were analyzed deriving from three patients, negative to naso‐oro‐pharyngeal swab for SARS‐CoV‐2. These COVID‐19–negative patients came to clinical observation due to urgent abdominal surgery that removed different sections of the digestive tract after thrombotic events. Immunohistochemical for the expression of SARS‐CoV‐2 combined with a panel of SARS‐CoV‐2 related proteins angiotensin‐converting enzyme 2 receptor, cluster of differentiation 147 (CD147), human leukocyte antigen‐G (HLA‐G), vascular endothelial growth factor (VEGF) and matrix metalloproteinase‐9 was performed. Tissue samples were also evaluated by electron microscopy for ultrastructural virus localization and cell characterization. The damage of the tissue was assessed by ultrastructural analysis. It has been observed that CD147 expression levels correlate with SARS‐CoV‐2 infection extent, vascular damage and an increased expression of VEGF and thrombosis. The confirmation of CD147 co‐localization with SARS‐CoV‐2 Spike protein binding on gastrointestinal tissues and the reduction of the infection level in intestinal epithelial cells after CD147 neutralization, suggest CD147 as a possible key factor for viral susceptibility of gastrointestinal tissue. The presence of SARS‐CoV‐2 infection of gastrointestinal tissue might be consequently implicated in abdominal thrombosis, where VEGF might mediate the vascular damage.