A method and an arrangement for automatic three-dimensional recording of structures of interest in a sample (15) are disclosed. The arrangement possesses a microscope having at least one microscope objective (13). The images of a sample (15) are acquired using a detector unit (19). A computer system (23) controls acquisition of the images and the microscope functions. The computer system (23) possesses a means (25) for automatically recording the entire marked specimen region in three dimensions.