Individual B dopant atoms residing beneath Si(001)-2 x 1 surfaces have been detected by scanning tunneling microscopy (STM). A subsurface B atom appears as a broad protrusion in filled-state images, while it appears as either a broad depression or a localized protrusion in empty-state images depending on the STM tip condition. This variation in dopant appearance is attributed to the different work function (WF) of the tip, i.e., the amount of tip-induced band bending differs depending on the tip WF, resulting in a different tunneling path and an opposite dopant appearance under the same bias voltage.