An automated high throughput apparatus, method and system for seed sampling is provided. The seed sampling system includes an ablation subsystem having a controlled cutting path and a seed handling subsystem comprising a staging system having a plurality of seed staging positions for staging a batch of seed in a sequential manner, and a carrier system for simultaneously presenting seed staging positions at the cutting path for removing a sample portion from each seed in the batch. A method of this invention includes providing ablation means having a controlled cutting path, automatically staging a batch of seed at a plurality of staging positions in a sequential manner, simultaneously presenting the batch of seed at the cutting path, and removing a sample portion from each seed in the batch.