The present study was aimed to observe the association of Vitamin B12 and folic acid with thyroid profile in pregnant women with overt hypothyroidism. 85 pregnant women with overt hypothyroidism were included in the study after obtaining written informed consent. Assessment of Free T3, Free T4 and TSH, folic acid and vitamin B12 was performed by standard methods. In first trimester, positive correlation was observed between vitamin B12 and FT3, which is statistically significant (r=0.505) (P < 0.0001). In second trimester, positive correlation was observed between vitamin B12 and FT3, which is statistically significant (r=0.510) (P < 0.0001). Negative correlation was observed between vitamin B12 and TSH, which is statistically significant (-0.229) (P < 0.05). Positive correlation was observed between folic acid and FT3, which is statistically significant (r=0.287) (P < 0.01). In third trimester, positive correlation was observed between vitamin B12 and FT3, which is statistically significant (r=0.486) (P < 0.0001). Negative correlation was observed between folic acid and TSH, which is statistically significant (r=-0.228) (P < 0.05). In cord blood samples, significant positive correlation was observed between vitamin B12 and FT3 (r=0.458) (P < 0.0001). Negative correlation was observed between folic acid and TSH, which is statistically significant (r=-0.257) (P < 0.05). We conclude that both Vitamin B12 and FA has significant negative correlation with TSH in all trimester while these have significant positive correlation with FT3, hence these values have to be monitored closely throughout the pregnancy for normal development of the fetus.