A sample cooling apparatus capable of cooling and holding samples or wafers at a cryogenic temperature with no vibration or drift with respect to a measurement reference surface is disclosed. In the sample cooling apparatus, a sample holder is arranged in a vacuum vessel mounted on a housing having a table for forming a measurement reference surface to be supported by a thermal insulator. A frame is disposed within the housing to be supported by a first buffer. A refrigerating machine is disposed in the frame to be supported by a second buffer and has a head directed to the vacuum vessel. The cooling head of the refrigerating machine is connected to the sample holder by way of a flexible thermal conduction member.