Objective:The reports about Factor V (FV) Leiden, Factor II (FII) G20210A and Methylenetetrahydrofolate reductase (MTHFR) C677T gene mutations of parents and fetal viability are frequently encountered in the literature, despite the fetal side of thrombophilia is scant. To clarify the three common thrombophilic gene mutations of the spontaneously aborted embryos, an accurate algorithm was followed to extract the fetal tissues and then the mutations were searched. Material and Methods:70 spontaneous abortion materials were included to the study and all were karyotyped. Cytogenetically abnormals were excluded from the study. To extract the fetal tissues, amplifications of sex determination region of chromosome-Y (SRY) gene and genotypings were performed, respectively. Extracted fetal tissues of spontaneous aborted embroys and parents were screened for the thrombophilic gene mutations via electronic microarray. Results:After excluding chromosomally abnormal and maternally contaminated ones totally ten fetal tissues were screened for the FII G20210A, FV Leiden and MTHFR C677T gene mutations, and two carry F II G20210A and F Leiden heterozygote mutations, and six carry heterozygote forms of MTHFR C677T. Conclusion:The present study performed on the limited number of abortion materials, has a value for distinguishing the fetal tissues before analyzing the three common mutation of thrombophilic genes which make the results are very substantial.