A transmission electron microscope makes it possible to search for defects without applying an undesirable treatment to a specimen by using a reference specimen prepared separately from a specimen to be observed. A pair of specimen holders detachable from the column of the electron microscope are adjacently arranged at upper and lower stages respectively along an electron beam axis to position the specimens closely to each other in an electron beam illuminating position. The pair of holders can be independently set to or removed from the electron beam illuminating position. The specimen holders include devices for selectively finely adjusting the spacing between the specimens, the angle of the specimen with respect to the electron beam axis and with respect to a plane perpendicular to the electron beam axis.