The adsorption geometry of cis-2-butene-1,4-diol (BEDO, HOCH(2)CH=CHCH(2)OH) on Si(100)-2 x 1 was studied using scanning tunneling microscopy (STM), high resolution X-ray photoemission spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Bias-voltage-dependent STM images exhibited features characteristic of two distinct BEDO adsorption geometries. One feature was a bright protrusion located on the center of a single dimer, indicating an on-top configuration. The low bias-voltage STM image clearly showed dark features indicative of the formation of Si-H bonds on adjacent dimers in the same dimer row. The other feature was a bright protrusion bridged on end between two adjacent dimers in the same dimer row, indicating an end-bridge configuration. Accompanying this feature, two dark features attributed to Si-H bonds were observed on opposite positions to the bridged protrusion. From the XPS results, the Si 2p core level spectra revealed that the dimer atoms are involved in the formation of Si-O and Si-H bonds. On the other hand, carbon K-edge NEXAFS spectra showed that the C=C bond does not participate in the adsorption reaction and remains as an unreacted group. Collectively, the experimental results indicate that the adsorption of BEDO on Si(100)-2 x 1 occurs through the formation of two Si-O bonds via nucleophilic reaction between the two OH groups of BEDO and two Si-Si dimers. Importantly, the maintenance of the C=C bond means that the C=C functional group can be utilized as a new reaction site for further surface chemical reactions.