An automated seed sampler system includes an imaging device for obtaining images of seeds, an orienting device for orienting the seeds based on the images, and a sampling station for removing tissue from the oriented seeds. In some aspects, the system also includes a transport subsystem for supporting the oriented seeds and conveying the oriented seeds to the sampling station. A method for removing tissue from seeds includes imaging the seeds, orienting the seeds based on image information obtained from the seeds, and removing tissue from the oriented seeds. In some aspects, the method also includes transporting the oriented seeds in a transport subsystem to a sampling station for removing the tissue from the oriented seeds, and/or collecting the tissue removed from the oriented seeds so that a one-to-one correspondence exists between the tissue and the sampled seeds, and/or analyzing the tissue for characteristics indicative of genetic and/or chemical traits.