A sample handling apparatus identifies sample holders and their location in a sample holder carrier. This information may be used to determine the identity of sample holders based only on location in the carrier during subsequent processing of material contained in the sample holders. Sample holder identity may be automatically read, and placement of holders in a carrier may be automatically determined and correlated with the holder identity. Such information may be stored, e.g., in a memory in the carrier so that sample holders can be easily identified later.