Purpose Vanished twin (VT) has been associated with poor perinatal outcomes. Our research aimed to investigate the outcomes of pregnancies with vanished twin and its possible association with methylenetetrahydrofolate reductase (MTHFR) polymorphisms. Methods This study consisted of 30 of 38 VT pregnancies (group 1, VT group), 109 singletons (group 2), 70 spontaneous twins (group 3), and 101 in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) twins (group 4). Results Most patients in group 1 (28/30) were tested for MTHFR genes (C677T or A1298C polymorphisms). Eight of the 38 pregnancies with VT (21.1%) resulted in miscarriage. The prevalence of B2 or more pregnancy losses^ in the Bobstetric history^ in group 1 was higher (23.3%) than those in the other groups (p =0.007,χ2 = 17.8). The allelic frequencies of MTHFR 677 and MTHFR 1298 in group 1 were 0.268 and 0.429, respectively (higher than those in healthy population). The median birthweights in groups 1, 2, 3, and 4 were 2940, 3200, 2300, and 2095 g, respectively. The prevalence of respiratory distress syndrome was significantly higher in the IVF/ICSI twin pregnancy group (p <0.001,χ2 = 21.2). Early pregnancy loss and the presence of B2or more miscarriages^ in the obstetric history of pregnancies with VT were more frequent. Conclusion The coincidence of VT and MTHFR polymorphisms might play an incidental or factual role in this connection.