Two isoforms of the ryanodine receptor subtype 3 (RYR3) have been described in smooth muscle. The RYR3 short isoform (RYR3S) negatively regulates the calcium-induced calcium release mechanism encoded by the RYR2, whereas the role of the full length isoform of RYR3 (RYR3L) was still unclear. Here, we describe RYR-dependent spontaneous Ca(2+) oscillations measured in 10% of native duodenum myocytes. We investigated the role of RYR3 isoforms in these spontaneous Ca(2+) signals. Inhibition of RYR3S expression by antisense oligonucleotides revealed that both RYR2 and RYR3L were able to propagate spontaneous Ca(2+) waves that were distinguishable by frequency analysis. When RYR3L expression was inhibited, the spontaneous Ca(2+) oscillations were never observed, indicating that RYR3S inhibited the function of RYR2. RYR2 expression inhibition led to Ca(2+) oscillations identical to those observed in control cells suggesting that RYR3S did not functionally interact with RYR3L. The presence and frequency of RYR3L-dependent Ca(2+) oscillations were dependent on sarcoplasmic reticulum Ca(2+) content as revealed by long-term changes of the extracellular Ca(2+) concentration. Our study shows that, in native duodenal myocytes, the spontaneous Ca(2+) waves are encoded by the RYR3L alone, which activity is regulated by sarcoplasmic reticulum Ca(2+) loading.