The vapor-phase synthesis of II–VI nanocrystals (quantum dots) has several advantages over traditional liquid-phase techniques, including better compatibility with existing operations in the microelectronics industry. On the other hand, it makes size control and surface passivation a more challenging task. In this paper we report the synthesis and surface passivation of luminescent ZnSe nanocrystals by reacting vapors of dimethylzinc:triethylamine (DMZ–TEA) adduct with hydrogen selenide gas (both diluted in hydrogen) in a counterflow jet reactor operating at 300 K and low pressures (120--60 Torr). The two reactants flow into a cylindrical chamber from separate inlets of a vertical opposed-flow configuration. Homogeneous nucleation of ZnSe occurs through an irreversible reaction between the precursors. The nuclei subsequently grow by surface reactions and cluster--luster coalescence to form nanocrystals that exhibit size-dependent luminescence. Surface passivation was achieved by introducing vapors of 1-pentanethiol into the reactor. The thiol vapors do not interfere with the nucleation and growth of the primary nanocrystals, but significantly change the morphology and size of the final coagulated particles collected on transmission electron microscopy (TEM) grids. The chemisorption of thiol vapors on the surface of the nanocrystals also leads to smaller degradation of the photoluminescence (PL) intensity after 1 month. Structural and morphological characterization of the particles was performed using HR-TEM, stoichiometric analysis using electron diffraction and Auger electron spectroscopy (AES), while PL and Raman spectroscopy were used to study their size-dependent optical properties.