The risk of fetal anomalies (FAs) is increased in infants of diabetic mothers. FAs are closely related to the glycosylated hemoglobin (HbA1c) level in pregnancy. To detect the prevalence of FAs in women with gestational diabetes mellitus (GDM). 157 pregnant women with GDM were included in this study, and data from 151 women were analyzed. Beyond the regular antenatal check-up, the HbA1c was checked monthly during the antenatal follow-up. Collected data after delivery were analyzed to detect the prevalence of FAs in women with GDM and the risk of FAs in relation to the pre-conceptional blood sugar and HbA1c. The FAs were recorded in 8.6% (13) of the 151 women with GDM. The recorded FAs were cardiovascular [2.6% (4)], musculoskeletal [1.3% (2)], urogenital [1.3% (2)], gastrointestinal [1.3% (2)], facial [0.7% (1)], central nervous system [0.7% (1)], and multiple FAs [0.7% (1)]. The uncontrolled pre-conceptional blood sugar significantly increased RR [RR 2.2 (95%CI: 1.7-2.9); P < 0.001], and odds of FAs [OR 17.05 (95%CI: 2.2-134.9); P = 0.007] in women with GDM. In addition, the HbA1c ≥6.5 significantly increased RR [RR 2.8 (95% CI: 2.1-3.8); P < 0.001], and odds of FAs [OR 24.8 (95% CI: 3.1-196.7); P = 0.002] in women with GDM. In this study, the prevalence of FAs in women with GDM was 8.6%. Uncontrolled pre-conceptional blood sugar and HbA1c ≥6.5 in the first trimester significantly increased the relative risk and the odds of FAs.