Vanadium pentoxide (V₂O₅) nanowires were directly transferred to desired patterns on SiO₂ substrates using the microcontact printing (MCP) technique. The hydrophilicity of the poly(dimethylsiloxane) (PDMS) stamp exerted a strong influence on the mechanism of transfer of polar V₂O₅ nanowires onto the substrate. The V₂O₅ nanowires were transferred from the relief side of the hydrophilic stamp, whereas they were transferred from the recess edges of the hydrophobic one forming agglomerated nanowire patterns on the substrate. When the hydrophobic stamp was used, the width of the agglomerated nanowire patterns could be controlled by the concentration of the nanowire solution as well as by the width of the recess area of the PDMS stamp. This method allows us to generate nanowire patterns with a submicrometre line width, which is much smaller than a the few-micrometre sizes of PDMS stamp patterns. When the hydrophilic stamp with a small-sized (≤ the average length of V₂O₅ nanowires) pattern was used, alignment of individual nanowires in the direction of the boundary of the line pattern was obtained. These results suggest that the transfer mechanism in the MCP process strongly depends on the wetting interaction between the stamp and the nanowire ink.