Fluoride (F) distributions in a synthesized hydroxyl apatite (HAp) block of uniform structure and in teeth were measured using in-air micro-PIGE (particle induced gamma-ray emission) and micro-PIXE system, which was developed at the Japan Atomic Energy Agency (JAEA) in Takasaki. We used a nuclear reaction 19F(p,αγ)16O to measure F density. The characteristic important feature of this technique is that it can measure F quantitatively in a microscopic area of the specimen placed in air. A surface of the HAp, the enamel buccal surface of a human molar, and a class V cavity wall in dentin were applied a sodium fluoride solution (NaF) four times and immersed in a normal saline solution. After one month, specimens were cut longitudinally. The F distributions were measured from the surface toward the inner part of the cut surface. The F penetration into specimens following NaF application was quantitatively configured in a two-dimensional mapping form. This method is quite useful for characterizing F distribution in a microscopic area of a tooth.