SNAREs (soluble NSF attachment protein receptors) are membrane proteins that catalyze membrane fusion. SNAREs are defined by a characteristic 70 residue sequence called the SNARE motif. During synaptic vesicle fusion, the single SNARE motif of the synaptic vesicle SNARE protein synaptobrevin/VAMP associates into a four-helical bundle with SNARE motifs from the plasma membrane SNARE proteins syntaxin 1 and SNAP-25. The four SNARE motifs (one each from synaptobrevin and syntaxin, and two from SNAP-25) assume a parallel orientation in the complex, suggesting that formation of the complex initiates fusion by forcing the membranes containing the SNAREs into close proximity. It has been proposed that SNARE complexes assemble in an N- to C-terminal progression, a process referred to as zippering, but little direct evidence for zippering exists. Furthermore, the SM protein Munc18-1, which binds to syntaxin 1 and is essential for synaptic fusion, is thought to prepare SNAREs for complex formation by an unknown mechanism, possibly by nucleating zippering. We now show that fragments containing the N- and C-terminal regions of the SNARE motif from syntaxin 1A bind SNAP-25 similarly. However, in permeabilized PC12 cells which are used as a biochemical model system to study synaptic fusion, only fragments containing the N-terminal region are powerful inhibitors of fusion. Furthermore, mutations in the N-terminal part of the Syntaxin SNARE motif have only a moderate effect on SNAP-25 binding but abolish the inhibitory activity of the SNARE motif. Finally, larger fragments of syntaxin 1A that strongly bind to Munc18-1 but do not readily assemble into SNARE complexes had no effect on exocytosis in permeabilized PC12 cells. Together these results suggest that Munc18-1 acts before SNARE complex assembly, and is no longer required at the stage of fusion assayed in permeabilized PC12 cells. The selective effect of the N-terminal half of the syntaxin 1A SNARE motif on PC12 cell exocytosis shows that the SNARE motif is functionally polarized, and supports the notion that SNARE complexes assemble in an N- to C-terminal zippering reaction during fusion without a stable, partially assembled intermediate.