ICSI bypasses not only fusion of the gametes but also a series of signalling events that occur in the sperm prior to and during interaction with the oocyte's vestments. The effect of this altered encounter of the gametes on the fertilization-associated intracellular calcium ([Ca2+]i) oscillations has not been thoroughly investigated. Here, ICSI and IVF were performed using gametes from two mouse strains, B6D2F1 and CD1, and in-vitro development, pattern of [Ca2+]i oscillations and down-regulation of inositol 1,4,5-trisphosphate receptor-1 (IP3R-1) in the produced embryos were compared. ICSI and IVF resulted in comparable rates of activation and pre-implantation development. However, ICSI-generated zygotes cleaved at a slower rate, had lower cell numbers and lower hatching rates. The deleterious effects of ICSI could not be exclusively attributed to the injury by the injection since sham-injected IVF zygotes only exhibited delayed progression to the blastocyst stage. ICSI and IVF induced similar initial [Ca2+]i responses, although ICSI zygotes exhibited shorter durations of [Ca2+]i oscillations and showed diminished degradation of IP3R-1. Importantly, sperm manipulation affected the pattern of oscillations, which further decreased pre-implantation developmental rates. Our results demonstrate that ICSI-induced [Ca2+]i responses are not equivalent to those initiated by IVF and that this may have developmental consequences.