Background: Gastrointestinal (GI) integrity/permeability were investigated as mechanisms for T-cell activation and poor immune recovery during cART (Immunological Non Responders, INR). Methodology: HIV+ patients (pts) on suppressive cART for at least 12 months were enrolled. 21 INR (ΔCD4 <30% and/or CD4 <350/uL) were compared to 29 Full Responders (FR). GI permeability (LAC/MAN test), stool microbiome (DGGE), plasma MT (LPS, sCD14, EndoCAb) and T-cell distribution (flow cytometry) were analyzed. 13 FR and 8 INR also underwent colonoscopy with colon and ileum biopsies for immunohistochemical (ICH) evaluation of adherens/tight junction proteins (CDh1, ZO-1, Claudin1 and 7), cell proliferation (Ki67), T-cell tissue count (CD3, CD4, CD8) and electron microscopy (EM) study of paracellular spaces. Anatomopathological (AP) findings were compared to those of 5 HIV- controls. Total (tHIV-DNA), integrated HIV-DNA (iHIVDNA) and 2-LTR circles were quantified by Real-Time PCR in colon/ileum biopsies and in blood isolated CD4 T-cells. Results: INR presented reduced naive CD4+CD45RA+ (p=.01) and CD4+CD127+ (p <.001) and increased activated CD8+CD38+ (p=.03) and CD8+CD38+RO+ (p=.03). INR and FR displayed comparable ileum and colon expression of CD3, CD4 and CD8. INR showed higher Ki67 colon expression (35%, IQR 30-40 vs 25%, IQR 9-30; p=.02). CDh1 and ZO-1 immunoreactivity were impaired in HIV+ pts vs controls. CDh1 immunostaining was distributed around the entire epithelial plasma membrane in controls, at the basolateral surface in FR and only at the basal level in INR. The lowest levels of CDh1 cells were detected in colon biopsies from INR. Moreover, ZO-1 expression was frequently negative in ileum and colon tissue from INR. EM evaluation of the colon confirmed wider intercellular spaces in INR (Fig). DGGE demonstrated clustering stool microbial communities in INR not detected in FR. Both INR and FR showed a heightened LAC/MAN ratio (>.045) suggesting increased GI permeability; however, no significant differences in LAC/MAN and plasma LPS, sCD14, EndoCAb were noted between groups. No differences in tHIV-DNA, iHIV-DNA and 2-LTR in circulating CD4 and colon/ileum tissue were registered between FR and INR. Conclusions: Patients failing CD4 recovery on effective cART present damage of gut junctional complexes seemingly not due to increased viral burden. Such defects may translate into impaired mucosal and peripheral immunity, hampering CD4 reconstitution, albeit GI CD4 repopulation.