For the first time, we observed the discrete distribution and fluctuation of active B dopants in scaled n-type MOSFETs (nFETs) and in various B-doped epilayers by the site-specific scanning spreading resistance microscopy (SSRM). The non-uniform B distribution observed in narrow and short-channel length nFETs may be the origin of threshold voltage fluctuations in nFETs. Significant B fluctuation at doping levels less than 2×1019 cm−3 was found in Si:B and Si:B/Si:P epilayers prepared at intermediate temperatures, indicating that this phenomenon is a particular characteristic of B dopants. The B fluctuation is attributed to segregation of B dopant, which depends on thermal diffusion and occurs even under thermal equivalent conditions without structural stress. Site-specific SSRM is demonstrated to be capable of observing discrete dopants in silicon.