dl-β-amino-butyric acid (BABA) has been found to protect potato plants against late blight caused by Phytophthora infestans. This paper compares gene expression profiles of a potato clone harboring horizontal resistance to P. infestans in response to BABA and the pathogen by using cDNA-amplified fragment length polymorphism (cDNA-AFLP), aiming at fudermental elucidation of molecular mechanisms of BABA induced resistance (BABA-IR). In total, 101 transcript derived fragments (TDFs) showed significant differential expression among the treated and their respective control samples. About half of differentially expressed fragments (49) were overlapped in both BABA and P. infestans induction systems, and homology analysis showed that these TDFs in common involved in signaling, cell wall strengthening and synthesis of antimicrobial compounds, reflecting both BABA-IR and the natural resistance shared similar defense mechanisms to a great extent. Analysis of the transcription profiles demonstrated that an early activation of plant basal defense system could be crucial for BABA-IR. Some differentially expressed TDFs homologous to genes encoding proteins related to jasmonic acid–and salicylic acid–dependent signaling pathways, were up-regulated by BABA. Similar genes associated with these pathways were also identified in the pathogen inoculated samples, reinforcing that the extensive cross-talk between BABA-IR and horizontal resistance may be important to coordinate the genes responsible for P. infestans infection in potato.