Cadmium (Cd) is a widespread soil contaminant that readily accumulates in wheat, and posing a potential threat to human health. Our aim is to investigate Cd toxicity effect and molecular mechanisms for wheat. In this study, the physiological indexes, morphology, and gene expression patterns of diploid wheat (Triticum urartu) seedlings were evaluated after 2 and 5 d of a Cd treatment (10 mu M CdSO4). The Cd treatment resulted in increased proline and glutathione contents in shoots and roots, slight damage to leaf tips, severe damage to root tips, and increased root secretions. Transcriptome analysis showed that there were significantly more differentially expressed genes (DEGs) in shoots and roots after 5 d of Cd stress than after 2 d of Cd stress, and the DEGs of the shoots were more different than the roots. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the pathways enriched under Cd treatment were "DNA replication" and "phenylpropanoid biosynthesis". These findings provide information about the responses to Cd stress in wheat, and provide a theoretical basis for reducing Cd toxicity and protecting food safety.