Autophagy is an evolutionarily conserved lysosomal pathway for degrading cytoplasmic proteins, macromolecules, and organelles, in addition to recycling protein and ATP synthesis. Although programmed cell death (PCD) is very important during embryogenesis, the mechanism underlying the dynamic development during this process remains largely unknown. In order to obtain insights into autophagy and it's relation with apoptosis in early embryo development, we first evaluated LC3 gene expression levels in mouse embryos developing in vitro. qRT-PCR revealed high expression levels from 1- to 4 cell stage embryo, and then expression decreased during morula and blastocyst formation. Indirect immunocytochemistry showed protein synthesis of LC3 in these stage embryos. Introducing of autophagy inhibitor, 3-MA (2mM) significantly decreased both developmental rate (54.85±11.0%) and total cell number (n=71±8), but increased apoptosis rate (5.68± 1.9%) at the blastocyst. Real time RT-PCR confirmed reduced expression of selected autophagy related genes, including ULK1, Atg4A, B, C, D, Atg5, Atg8, Gabarap, Atg9A, B and Atg16L. Treatment of autophagy inducer, rapamycin (50 ng/㎖) increased both mRNA expression and protein synthesis of LC3 and apoptosis rate (16.11±3.42%), but decreased developmental rates (50.16±9.78) and total cell numbers (n=60±7) as compared to control developmental rate (70.74±12.9%), Total cell number (89.8±9) and apoptotic cell death (1.11±0.7%). These results suggest that autophagy is related with apoptosis in mouse embryo, which possibly give a role for early development.