An X-ray analyzer includes a transmission X-ray inspecting portion having a first X-ray source and a transmission X-ray detector for detecting a transmission X-ray that passed through a sample from the first X-ray source, and a fluorescent X-ray inspecting portion having a second X-ray source and a fluorescent X-ray detector for detecting a fluorescent X-ray output from the sample when the sample is irradiated with an X-ray from the second X-ray source. A movement mechanism moves a sample stage that supports the sample. A foreign matter position calculating unit calculates a position of foreign matter in the sample, and a movement mechanism control unit controls the movement mechanism so that the position of the foreign matter calculated by the foreign matter position calculating unit coincides with an optical axis of the second X-ray source.