Several classes of proteins have been identified that mediate and regulate membrane dynamics throughout the eukaryotic cell. One class of membrane-trafficking proteins, referred to as soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs), have been implicated in mediating membrane fusion. Here we characterize syntaxin 11, an atypical syntaxin family member lacking a transmembrane domain. Syntaxin 11 was found to be enriched in tissues of the immune system including thymus, spleen and lymphnodes; however, lower levels of the protein are found in other tissues. Using immunofluorescence and electron microscopy techniques, we demonstrate that syntaxin 11 associates with intermediate compartment (IC) and post-Golgi membranes through a putative palmitoylation domain, as well as through formation of the 100-kDa complex with, as of yet, unidentified proteins. The coiled-coil forming H3 domain is required for the formation of the 100-kDa complex, and this complex can be dissociated upon addition of alphaSNAP. Thus, while the precise function of syntaxin 11 remains to be elucidated, it may be particularly important in regulating membrane dynamics of the immune system.