Background: In general, miscarriage is one of the most common complications of pregnancy and it is the pregnancy loss before 20 weeks of gestation or birth weight below500 grams. Recurrent Pregnancy Loss is defined as two or more spontaneous miscarriages. Genetic disorders such as mutations can be involved in miscarriage. Considering the importance of this issue, in this study, G1691A mutation of coagulation factor 5 and common deletion mutation in the mitochondrial genome(4977-bp deletion in mtDNA) were investigated as factors which can influence miscarriage, especially recurrent miscarriage. Materials and Methods: For this study 41 patients with the history of miscarriage and 48 healthy women with successful delivery were selected and completed the questionnaires which included questions such as miscarriage history, age, blood type and then Blood samples were taken. After extraction of DNA from each sample, the studied mutations were determined using PCR method. At the end, analysis of the results and assessment of other important and effective factors in them was done using Epi Info software and using chi square (X2) test. Results: Among the patients ,there were 29.25% patients with one miscarriage, 65.85% patients with two miscarriages and 4.9% patients with three miscarriages. There was no homozygous genotype in the study of G1691A mutations in both groups, and prevalence of heterozygotes was 17% among patients and 4.17% among controls. On the other hand, frequency of 4977-bp deletion in mtDNA in patients group and control group was 68.29% and 14.58%, respectively. Analysis showed that frequency of G1691A mutations and common deletion mutation in mtDNA in patients group were higher than controls and were statistically significant . Although the opportunity to have miscarriage in GA genotype and carriers of common deletion is more than control, but there is not any correlation between these two mutations and their inheritability and also they have not affected each other. Therefore, we can use the above mutations as a molecular marker for early detection and timely treatment in patient’s likelihood of miscarriage.