An automated system for sampling seeds generally includes an automated sampling station having a seed feeder and a seed sampler. The seed feeder is configured to deliver seeds to the seed sampler, and the seed sampler is configured to remove material from the seeds without substantially adversely affecting the germination viability of the sampled seeds. The system also includes a sample handling station configured to receive the material removed from the seeds, and a seed handling station configured to receive the sampled seeds after the material is removed from the seeds such that the relationship between the material removed from the seeds and the respective seeds can be determined.