Simultaneous fluorescence-topographic nanoscale imaging of cell-surface molecules in the context of membrane ultra-structures has not been reported. Here, near-field scanning optical microscopy (NSOM)-based direct fluorescence-topographic imaging indicated that GM3 rafts/ nanodomains (190.0 6 49.8 nm ranging 84.5-365.0 nm) were localized predominantly on the peaks of microvillus-like protrusions in the apical membrane of GM3 1 Madin-Darby canine kidney cells, whereas GM1 rafts/nanodomains (159.5 6 63.8 nm ranging 42-360 nm) were distributed mainly on the slops of protrusions or the valleys between protrusions in the plasma membranes of GM1 1 MDCK cells. The data demonstrated that gangliosides polarized not only in a well-known apical-basolateral manner but also in the more microscopic peak-valley manner, implicating unique distribution of GM1 or GM3 in cell-surface fluctuations on the apical membrane of polarized cells. The peak-valley polarities of gangliosides also implicated their different functions relevant to lipid rafts, microvilli, or cellular processes. Importantly, our study demonstrated for the first time that the NSOM-based direct fluorescence-topographic imaging is unique and powerful for elucidating nanoscale distribution of specific cellsurface molecules in membrane fluctuations.-Chen, Y., J. Qin, and Z. W. Chen. Fluorescence-topographic NSOM directly visualizes peak-valley polarities of GM1/GM3 rafts in cell membrane fluctuations. J. Lipid Res. 2008Res. . 49: 2268Res. -2275 Supplementary key words near-field scanning optical microscopyMorphological, chemical, and functional polarities of membrane lipids (1) are well described and are relevant to lipid raft formation and cellular signaling. While different lipid components, especially glycolipids, are distributed in the apical-basolateral manner in the plasma membranes of epithelial cells (2), the ganglioside-enriched rafts on T lymphocytes can redistribute asymmetrically in a leadingedge-uropod manner upon cell activation (3). Despite identification of apical-basolateral and leading-edge-uropod distributions of membrane lipids, little is known about nanostructures and precise topographic localization of gangliosides or lipid rafts in the context of biological membrane ultrastructures, such as microvilli or protrusions/valleys.Widely used conventional imaging techniques have a limited capability to elucidate fluorescence-topographic distribution of cell-surface molecules at nanoscale. The traditional fluorescence instruments including confocal microscopy do not have enough optical resolution for detection of nanscale ganglioside clusters. Fluorescence resonance energy transfer measurement or single particle tracking technique is unable to reveal the nanoscale topographic localization of molecules on membrane surface. Rapidly developed atomic force microscopy fails to detect fluorescence information. The high-resolution electron microscopy (EM) is often limited by uncertain fidelity or reliability due to the complicated sample-preparing ...