The transcription factor Pdr1p recognizes Pdr1p/Pdr3p‐response element (PDRE) to activate genes involved in multidrug resistance of the budding yeast. To identify novel targets of Pdr1p, we compared transcriptomes among the yeast cells bearing wild, disrupted and gain‐of‐function alleles of PDR1 using a high‐throughput fluorescent differential display PCR. Consequently, we identified 20 transcripts apparently regulated by Pdr1p, which are derived from well‐known target genes as well as those that have never been described in the context of drug resistance. Intriguingly, among the latter, a previously unrecognized gene bearing a small putative open reading frame preceded by a functional PDRE was found.