The present invention is related with the field of the medicine, particularly with the use of an APL peptide or its analogues derived from the human heat shock protein of 60 kDa, for the manufacture of a pharmaceutical composition for the treatment of Crohn's disease, ulcerative colitis and diabetes mellitus type 1. This peptide is biodistributed into the gastrointestinal tract and also promotes the induction of apoptosis in activated intestinal lamina propria and peripheral blood T cells of patients with Crohn's disease. Furthermore, this peptide induces apoptosis in mononuclear cells of patients with diabetes mellitus type 1.