During cell cycle progression, somatic cells exhibit different patterns of intracellular calcium signals during the G0 phase, the transition from G1 to S and from G2 to M. Because pluripotent embryonic stem (ES) cells progress through cell cycle without the gap-phases G1 and G2 we aimed to determine if ES cells still exhibit characteristic changes of [Ca²⁺]_i during cell cycle progression. With confocal imaging of the Ca-sensitive dye Fluo-4/AM we identified that undifferentiated mES-cells exhibit spontaneous Ca-oscillations. In control cultures where 50.4 % of the cells reside in the S-phase of the cell cycle, oscillations appeared in 36 % of the cells within a colony. Oscillations were not initiated by Ca-influx but depended on IP₃ mediated Ca-release and the refilling of intracellular stores by a store operated Ca-influx (SOC) mechanism. Using cell cycle synchronization, we determined that Ca-oscillations were confined to the G1/S phase (~70% oscillating cells vs. G2/M: ~15 % oscillating cells) of the cell cycle. ATP induced Ca-oscillations, and activation of SOC entry could be induced in G1/S and G2/M synchronized cells. Intracellular Ca-stores were not depleted and all three IP₃ receptor isoforms were present throughout the cell-cycle. Cell cycle analysis after EGTA, BAPTA/AM, 2-APB, thapsigargin or U-73122 treatment, underlined that IP₃ mediated Ca release is necessary for cell cycle progression through G1/S. Because the IP₃ receptor sensitizer thimerosal induced Ca-oscillations only in G1/S we propose that changes in IP₃R sensitivity or basal levels of IP₃ could be the basis for the G1/S confined Ca oscillations.