Pulmonary hypertension is a serious disease associated with constriction, cellular proliferation, inflammation, and in situ thrombosis of the small vessels of the lung. Some studies suggest that homozygous 677TT variants and compound heterozygous 677CT/1298AC variants in methylenetetrahydrofolate reductase may increase the risk for systemic vascular disease. We sought to determine the prevalence of variants in methylenetetrahydrofolate reductase in patients with pulmonary hypertension, and whether homozygous or compound heterozygous variants are associated with an increased severity of disease. The medical records of patients with pulmonary hypertension were retrospectively reviewed to identify 105 patients who were evaluated for variants in methylenetetrahydrofolate reductase. The frequency of the minor allele 677C > T was 0.352 and the frequency of the minor allele 1298A > C was 0.295. The number of patients who were homozygous 677TT, homozygous 1298CC or compound heterozygous 677CT/1298AC was similar to the number of control patients with corresponding variants in a meta-analysis of studies. Patients with homozygous or compound heterozygous variants had a significantly higher ratio of pulmonary to systemic vascular resistance (0.75 ± 0.07 vs. 0.56 ± 0.04, p = 0.019) during baseline heart catheterization. Twenty-five of 61 patients without, and 28 of 44 patients with, homozygous or compound heterozygous variants had moderate to severe disease (p = 0.030). Variants in methylenetetrahydrofolate reductase are common in the general population and in patients with pulmonary hypertension. It is unlikely that these variants cause pulmonary vascular disease; however, they may influence the progression or severity of disease.