Methylene tetrahydrofolate reductase (MTHFR) is an enzyme involved in the metabolism of homocysteine to methionine, and folic acid is an essential cofactor. Mutations in the MTHFR gene lead to hyperhomocysteinemia and vascular thrombosis. Heterozygous mutation involving a single nucleotide polymorphism in the MTHFR gene leading to vascular thrombosis is very rare. We present a case of segmental renal artery thrombosis secondary to this mutation and to the best of our knowledge, it is the first case to be reported. Though easily treatable, this is a condition which is seldom investigated in the workup of thrombotic disorders.