The transcription factor NF-kappaB can be activated in different forms, including transcriptional activating and repressing forms. Intestinal epithelial cells have been found to modulate the relative levels of the p65-p50 and p50-p50 NF-kappaB complexes in a number of instances, and here we show that this ratio was altered in response to dietary fiber (wheat bran) and carcinogen exposure (azoxymethane). The influence of these complexes on gene regulation was examined in more detail in cell culture models. The colon-derived HT-29 cell line likewise activated both p65-p50 and p50-p50 NF-kappaB complexes: TNF-alpha triggered a strong, sustained p65-p50 activation with lower relative levels of p50-p50, whereas IL-1beta transiently activated p65-p50 with higher relative levels of p50-p50. Transfection experiments with an NF-kappaB reporter plasmid indicated that p50 was a repressor in HT-29 cells. Increased expression of the p50-p50 dimer by an adenovirus showed that the p50-p50 dimer suppressed IL-1beta activation of endogenous genes more than 5-fold (TNF-alpha, Cox-2 and IL-8), whereas gene activation by TNF-alpha was not significantly affected. DNA binding analyses showed a number of strong p50-p50 binding sites on these promoters. The selective p50-p50 suppression of IL-1beta gene activation corresponded to the transient nature of p65-p50 activation induced by IL-1beta (in both HT-29 and Caco-2 cells). Our findings demonstrate a novel gene regulatory mechanism for the NF-kappaB p50-p50 complex: a signal-specific transcriptional repression that appears to selectively inhibit stimuli that transiently activate p65-p50 complexes.