In accordance with the present invention, there is provided a pattern defect detecting apparatus using a scanning and transmission electron microscope, comprising an electron gun for accelerating an electron beam with high energy enough to transmit it through a sample and for radiating the accelerated electron beam, a condenser lens for focusing the electron beam generated by said electron gun, a beam deflection coil for deflecting the electron beam focused by said condenser lens, an objective lens for further focusing the electron beam deflected by said beam deflection coil onto a fixed spot, an XY stage for disposing the sample so as to be opposed to said objective lens, said XY stage being movable in X and Y directions in a step and repeat manner, a sample chamber for housing the XY stage in vacuum, said sample chamber including at least the outlet of the electron beam of said objective lens, an electron beam detector for detecting electron beams transmitted through said sample, said electron beam detector being fixed to a stationary member such as said chamber or a lens barrel, and defect detecting means for scanning the electron beam by using said beam deflection coil for each step and repeat operation of said XY stage, for comparing a video signal obtained from said electron beam detector with a reference pattern read out from memory means, and for thereby detecting a defect of the sample.