Most current research in the field of adventitious shoot formation is focused on the regulatory function of a single gene. However, a systematic transcriptomic analysis of the early adventitious shoot formation is still lacking. Here, we analyzed the transcriptome profiling of the early adventitious shoot formation in Arabidopsis by RNA-seq high throughput sequencing technology, and identified 2 457 differentially expressed genes. Detailed categorization revealed that these genes were mainly involved in hormone homeostasis or signal transduction, callus and lateral root formation, shoot apical meristem development and photosynthesis. Further pathway enrichment analysis showed that genes involved in phenylalanine metabolism and phenylpropanoid biosynthesis were significantly enriched. Moreover, exogenous phenylalanine could repress adventitious shoot formation, indicating that phenylalanine metabolism and phenylpropanoid biosynthesis might be important for adventitious shoot formation.