This study was conducted to investigate mitochondrial, nuclear chromatin and cytoskeletal organisation of vitrified embryos based on timing of the first zygotic cleavage. Embryos were retrieved from superovulated ICR mice, 28 hours after hCG injection. Two-cell stage embryos were categorised as early-cleaving (EC), while zygotes with 2-pronuclei as late-cleaving (LC) embryos. Embryos were cultured overnight in M16 medium supplemented with 3% bovine serum albumin (BSA) in carbon dioxide incubator. After 20 hours, the embryos were vitrified for one hour and warmed to room temperature. They were then fixed and immunostained to visualise distribution and intensity of mitochondria, nuclear chromatin and cytoskeleton. Finally, the embryos were mounted on glass slides and examined under a Confocal Laser Scanning Microscope (CLSM). Fluorescence intensities were analysed using LAS-AF-Lite Software. Results showed that EC embryos had significantly higher mitochondria (39.22 ± 12.50 versus 35.42 ± 14.61 pixel, p<0.05) and actin filaments fluorescence intensities (11.43 ± 5.44 versus 5.23 ± 2.20 pixel) compared to LC embryos (p<0.001). There was no significant difference in nuclear chromatin and microtubules fluorescence intensities between EC and LC embryos. These findings suggest that greater cryosurvivability of vitrified EC compared to LC embryos was contributed by higher densities of mitochondria and actin filaments. Thus, selection of embryos for IVF procedure should be made based on timing of the first zygotic cleavage.