The intestinal epithelium acts as a physical barrier between the gut and the bloodstream. Leakage of solutes across the epithelium is restricted by specialized cell–cell junctions, called septate junctions (SJs) in invertebrates. In their paper, Yasushi Izumi, Kyoko Furuse and Mikio Furuse (Izumi et al., 2019) now characterise smooth septate junctions (sSJs), an endodermally derived subtype of SJs. The authors find that conditional depletion of sSJ proteins in adult Drosophila causes a reduction in fly lifespan and interferes with midgut barrier function. Furthermore, absorptive enterocytes frequently enter the midgut lumen, display polarity defects and accumulate in the most posterior part of the midgut, causing intestinal hypertrophy. The authors show that this phenotype is likely to be caused by an increased number of intestinal stem cells (ISCs), which can differentiate into enteroblasts, the immediate precursors of enterocytes. ISCs overproliferate upon depletion of sSJ proteins owing to overactivity of the Ras-MAPK and Jak-Stat signalling pathways. Consequently, mutation of Jak-Stat pathway activators in cells with defective sSJs prevented hypertrophy in the posterior midgut. However, ISC proliferation in these flies was nonetheless increased, leading the authors to speculate that mutation of Jak-Stat activators reduces the number of enterocytes by preventing enteroblast differentiation. Thus, this study illustrates the role of sSJs in maintaining tissue homeostasis in the invertebrate gut and introduces a new model to study intestinal barrier dysfunction in Drosophila.