Recurrent miscarriage (RM) affects 1-3% of couples. So far, diagnostic procedures are performed only in female patients. However, the main part of the placentary perfusion is encoded by both the maternal and the paternal genome.In this case-control study, German couples with two (n = 49) or three and more RM (n = 102) and 157 German control couples were analyzed for the factor V-Leiden 169 1G > A mutation (FVL), the prothrombin (PT) 202 10G > A substitution, and the 677C > T replacement in the 5, 10-methylenetetrahydrofolate reductase (MTHFR) gene.No significant differences in the prevalence of the FVL, PT or MTHFR mutation were observed in male partners of RM patients and in control men [RM/control: FVL heterozygous 13/151 (8.6%): 14/157 (8.9%) (P = 0.9); PT heterozygous 2/151 (1.3%): 7/157 (4.5%) (P = 0.097); PT homozygous 0/151: 2/157 (1.3%); MTHFR homozygous 19/151 (12.6%): 18/157 (11.5%) (P = 0.12)]. This was also true for female RM patients. However, miscarriage during the embryonal period (5-10 weeks of gestation) was significantly associated with a maternal heterozygous FVL mutation (P = 0.014).Recurrent miscarriage was not associated with paternal thrombophilia. Men of the control group showed an even higher incidence of the PT and MTHFR mutations. Abortions in the embryonic phase of fetal development were associated with a significantly higher incidence of maternal heterozygosity for FVL.