This study documents differences in ligand binding and signal transduction properties between the human (h) 5-hydroxytryptamine (5-HT) 4a and h5-HT 4b receptor splice variants stably expressed in human embryonic kidney 293 cells. The fraction of the [ 3 H]5-HT high-affinity site relative to the whole receptor population measured with [ 3 H]GR113808 was higher for the h5-HT 4a isoform (around 0.4) than for the 5-HT 4b isoform (around 0.2) and was independent of the level of expression. The potency and efficacy of reference compounds tested for the cAMP response differed slightly but significantly between both variants. Most remarkably, 5-methoxytryptamine and prucalopride were found more potent on the 5-HT 4b variant, whereas SDZ-HTF 919 and SB204070 were more potent on the 5-HT 4a variant. Guanosine-5Ј-O-(3-[35 S]thio)triphosphate binding on membranes and cAMP assays in whole cells revealed that only the h5-HT 4b isoform coupled to G␣i/o-proteins in addition to its well-documented G␣s coupling. In contrast, the h5-HT 4a receptor coupled only to G␣s-proteins, however, was able to trigger an increase in the intracellular calcium concentration ([Ca 2ϩ ] i ). The observed [Ca 2ϩ ] i increase did not occur through inositol phosphate formation and was not sensitive to Bordatella pertussis toxin, forskolin, or 3-isobutyl-1-methylxanthine (pre)treatment but was due to Ca 2ϩ influx from the extracellular environment. Interestingly, the Ca 2ϩ pathway was dependent on high receptor expression levels and was compound-specific, because benzamide-like compounds triggered two to three times higher responses than indoleamines. Taken together, these data provide the first evidence for fine functional differences between C-terminal splice variants of the h5-HT 4 receptor, which may contribute to a better understanding of the functional diversity of this receptor class.The ubiquitous neurotransmitter 5-hydroxytryptamine (5-HT, serotonin) has so far been shown to interact with seven receptor classes, classified as 5-HT 1 to 5-HT 7 receptors.