The RAG3 gene of Kluyveromyces lactis, a homolog of PDC2 of Saccharomyces cerevisiae, is known to be a regulator of the pyruvate decarboxylase gene KlPDC1. We have identified new target genes for Rag3p. The RAG3 gene product was found to be required for the transcription of two genes of the biosynthetic pathway of thiamine (a cofactor of pyruvate decarboxylase). Conversely, the RAG3 gene product partially repressed the expression of the pyruvate dehydrogenase gene KlPDA1. Therefore, RAG3 may act as a general regulator in the balance of the two alternative pathways of pyruvate metabolism in yeast.