Aims To compare gestational diabetes mellitus (GDM) risk among two ethnic minority groups, with high type-2 diabetes (T2DM) prevalence, as compared to the Jewish population majority group. Methods A historical cohort study was conducted using clinical data collected between January 1, 2007, and December 31, 2011. The study sample included 20–45-year-old women; 2938 Ethiopian, 5849 Arab and 5156 non-Ethiopian Jewish women. GDM was defined according to the two-step strategy: step 1: glucose ≥ 140 mg/dl and step 2: using Coustan and Carpenter’s diagnostic criteria. GDM risk was tested in a multivariable model, adjusted for age, parity and pre-gestational values of the metabolic syndrome components. Results Mean body mass index (BMI) values and morbid obesity rates were lowest among Ethiopian women and highest among Arab women. The prevalence of pre-gestational diabetes was significantly higher among Ethiopian (2.7%) and Arab (4.1%) women than among non-Ethiopian Jewish women (1.6%), and GDM screening rates were relatively high (85.5%, 87.2% and 83%, respectively). The proportion of pregnancies complicated with GDM was higher among Ethiopian women (4.3%) but not significantly different between Arab (2.9%) and non-Ethiopian Jewish (2.2%) women. In multivariable analysis, GDM was associated with Ethiopian ancestry (OR, 2.55; 95% CI, 1.60–4.08), adjusted for age, BMI, plasma triglyceride level and parity. Arab ethnicity was not significantly associated with GDM risk in multivariable analysis. Conclusions Both Ethiopian and Arab minority ethnicities have a higher risk of T2DM in comparison with other Israeli women, but only Ethiopian origin is an independent risk factor for GDM while Arab ethnicity is not.