We describe a new endoplasmic reticulum (ER)-associated stress response in the filamentous fungus Aspergillus niger. The inhibition of protein folding within the ER leads to cellular responses known collectively as the unfolded protein response (UPR) and we show that the selective transcriptional downregulation of the gene encoding glucoamylase, a major secreted protein, but not two non-secreted proteins, is an additional consequence of ER stress. The transcriptional downregulation effect is shown by nuclear run-on studies to be at the level of transcription, rather than mRNA stability, and is found to be mediated through the promoter of gIaA in a region more than 1 kb upstream of the translational start. The inhibition of protein folding in the ER can be induced in a variety of ways. We examined the effects of dithiothreltol (DTT), a reducing agent that causes the formation of unfolded proteins. Although a general downregulation of transcription was seen with DTT treatment, we show that selective downregulation was observed with the gIaA, gene compared with genes encoding the non-secreted proteins γ-actin and glyceraldehyde 3′-phosphate dehydrogenase. The DTT-treated fungal cells also showed evidence for the induction of the UPR because expression of bipA and pdiA, encoding an ER-resident chaperone and foldase, respectively, are upregulated and splicing of hscA, the gene encoding the transcription factor responsible for induction of the UPR, occurs allowing the production of an active HacA protein. As a preliminary attempt to investigate if the transcriptional downregulation effect was mediated through HacA (i.e. part of the UPR), we examined ER stress induced through antisense technology to lower the level of PDI in the ER of A. niger. Although the transcription of gIaA was attenuated in that strain of A. niger, UPR was not evident, suggesting that the transcriptional downregulation mechanism is controlled differently from the UPR.