Introduction: Gastrointestinal infections are one of the leading causes of morbidity and mortality throughout the world, particularly in the immunocompromised. Gastrointestinal PCR appears to be the technique of choice for establishing the molecular diagnosis of pathogenic gastrointestinal agents. The aim of this study was to establish the epidemiological, clinical and evolutionary profile of gastrointestinal infections and to study the impact of molecular diagnosis on the choice of a targeted therapy. Methods: This is a retrospective study carried out in the Microbiology Department of Arrazi Hospital of the Mohamed VI University Hospital Center, including all immunocompromised patients treated for a gastrointestinal infection and needing a hospitalization in the various departments, over a period of 15 months. Results: During the period studied, 124 patients were collected. The average age of the patients was 22 years. Signs of gastrointestinal infection were present in all patients. Of the patients sampled, 95.2% received probabilistic antibiotic therapy. Gastrointestinal infection has been documented in 57.26% of patients. A bacterial etiology was found in 76.81% of patients. A viral etiology was found in 13.04% of the patients and a parasitic etiology was found in 10.15% of the patients. Enteropathogenic E. coli was the most common infectious agent detected (19.53%). Co-infections were found in 29.84% of patients. Following PCR results, management was changed in 70 patients (56.45%), including initiation or modification of antibiotics in 40 patients (32.26%) and discontinuation of antibiotic therapy in 30 patients (24.19%). Conclusion: The diagnosis of gastrointestinal infections by multiplex PCR allowed us to provide optimal patient care with a reduction in the unnecessary use of antibiotics and an improvement in the course of care.