Cytoplasmic fragmentations are frequently observed in early mammalian embryos, and especially in the human. In our research we have observed subtle clues that the occurrence of fragmentation was most likely a result of somatic cell nuclear transfer (NT) protocols, and in particular, the in vitro culture system. In this study we examined various putative factors that might induce early embryo fragmentation in the ovine. The results indicate that nuclear transfer protocols such as the fusion parameter, activation treatment, and especially the choice of culture medium affected embryo cleavage rates and resulted in a higher incidence of fragmented embryos. Upon using the same fusion parameter, activation parameters that were based upon amino acids containing synthetic oviduct fluids (SOFaa) culture system resulted in significantly lower fragmentation rates than when utilizing a Charles Rosenkrans 1 (CR1aa) culture system. Fragmented embryos typically exhibited irregular numbers of blastomeres with the majority of blastomeres devoid of chromatin. Factors such as fusion DC pulse, activation treatment and culture system led to higher fragmentation and also affected in vitro and in vivo embryo development. The SOFaa based culture system produced a higher number of quality NT embryos resulting in higher pregnancy rates and the birth of live lambs as compared to the CR1aa based system ( P < 0.05). We conclude that early embryo fragmentation in the ovine is caused by suboptimal cloning protocols, and NT embryo development is especially affected by the culture system used.