The presence of pathological alleles of single nucleotide polymorphisms (SNP) of the folic acid cycle genes is one of the female reproductive system violation factors including habitual miscarriage and pre-eclampsia. The realizing mechanism for this genetic predisposition is hyperhomocysteinemia-homocysteine level increasing in the blood. This study presenting an attempt to find the relationship between the genotype for the four SNPs of the three folate cycle genes-C677T and A1298C of the MTHFR gene, A2756G of the MTR gene and the A66G of the MTRR gene and the homocysteine level in the blood of women with impaired pregnancy. As a result no direct correlation was found but it was found a statistically significant interlation between the presence of pathological alleles of the studied SNP and the mean square deviation (σ) of the homocysteine level fluctuations over time. For the polymorphism C677T of the MTHFR gene σ of the homocysteine blood level fluctuation is increased up to four times in women with a homozygous pathological state TT compared with the normal homozygotes CC. The clinical importance of monitoring the homocysteine blood level has been shown especially for women with folate cycle genes pathological alleles' presence.