Membrane contact sites (MCSs) are domains formed by the close proximity of two membranes from distinct organelles, and are where metabolites and information are exchanged. To understand the importance of these sites, it is essential to identify their molecular components. Here (p. 5500), Fabien Alpy, Catherine Tomasetto and colleagues investigate the role of the two related late-endosomal membrane-anchored proteins StAR-related lipid transfer domain-3 (STARD3) and STARD3 N-terminal like (STARD3NL) in the formation of MCSs between the endoplasmic reticulum (ER) and late endosomes. Using ultrastructural studies, the authors first show that both STARD3 and STARD3NL can induce the formation of MCSs between late endosomes and the ER. They next establish the presence of a conserved FFAT-like motif in the sequences of both proteins, and show that these motifs interact with ER-resident VAMP-associated proteins (VAPs) across the MCSs between late endosomes and the ER. Moreover, the extensive late-endosome–ER contacts mediated by the presence of STARD3NL proteins and VAPs alter the formation of endosomal tubules. Finally, using an in situ proximity ligation assay, the authors demonstrate the formation of late-endosome–ER MCSs by the endogenous proteins – the first report of this contact site being visualised by light microscopy without the need for overexpression. Taken together, these data describe a novel molecular tether, formed by either STARD3 or STARD3NL and VAP, at sites of close membrane apposition between late endosomes and the ER.