Problem: Recurrent pregnancy loss (RPL) is a heterogeneous disorder. The contribution of specific thrombophilic genes to the pathophysiology of RPL has remained controversial. We evaluated the prevalences of 12 thrombophilic gene mutations among homogenous Caucasian couples with RPL and fertiles. Method of study: This was a prospective case-control study evaluating 272 women with RPL and 152 of their male partners, and a control group of 56 fertile couples. We investigated mutations including FV Leiden, factor V H1299R, factor II prothrombin G20210A, F XIII V34L, β-fibrinogen -455G>A, plasminogen activator inhibitor-1, GPIIIa L33P (HPA-1 a/b L33P), MTHFR C677T, MTHFR A1298C, ACE I/D, Apo B R3500Q, and Apo E. Results: Overall, heterozygous mutations of FV Leiden, FXIII V34L, GPIIIa L33P, Apo E4, and prothrombin G20210A and homozygous mutations of PAI-1and MTHFR C677T were associated with RPL. There was no meaningful association between RPL and other studied genes. Conclusion: In contrast to the other mutations and polymorphisms, FV Leiden, FXIII V34L, GPIIIa L33P, Apo E, prothrombin G20210A, PAI-1 and MTHFR C677T gene mutations may help to identify the couples at risk for recurrent pregnancy loss. © 2009 John Wiley & Sons A/S.