The murine 5-HT(3A) receptor subunit is expressed as either of two splice variants which are differentially regulated in vivo. The difference resides in a six-amino acid sequence within the cytoplasmic loop between transmembrane regions 3 and 4, which is present in the long form but not the short form. No physiological roles have yet been ascribed to the two splice variants. Whole cell patch clamp recording from transfected HEK 293 cells stably expressing either long or short form receptors showed very similar responses under control conditions. However, inclusion of 1 mM cAMP (activator of protein kinase A) in the patch pipette caused an initial increase in the desensitization rate of the long form, but a decrease in the short form. With the addition of 100 nM phorbol 12-myristate 13-acetate (PMA; activator of protein kinase C) to the pipette solution, responses elicited with 1 microM 5-HT revealed an increase in the current amplitude in the long but not the short form of the receptor. Over a longer time period, inclusion of PMA in the patch-pipette caused a faster run down of peak current amplitude in response to 30 microM 5-HT in the long form but did not affect the short form; there was no observed long-term effects of cAMP. We conclude that the long and short forms of the 5-HT(3) receptor are differentially modulated by agents that activate PKA and PKC. These different patterns of modulation could have markedly divergent consequences on receptor function.