Background Gestational diabetes mellitus (GDM) is a big health problem that adversely affects both the maternal and perinatal outcomes. We aimed to predict the development of GDM in the first trimester using high sensitivity C-reactive protein (hs-CRP) and serum magnesium. Methods The study conducted in the antenatal care clinic of Saad Abualila Hospital (Khartoum, Sudan). Pregnant women were enrolled in this longitudinal cohort study during first trimester ≤14 weeks of gestation. Serum hs-CRP and magnesium concentrations were measured between weeks 11 and 14 of gestation. Glucose tolerance test and fasting plasma insulin (FPI) measurement were performed between 24 and 28 weeks gestational age. To assess insulin sensitivity and β-cell function, Homeostatic Model Assessment Insulin Resistance (HOMA-IR), HOMA-β indices and Quantitative Insulin Sensitivity Check Index (QUICKI) were calculated and used. Results Out of the 126 who completed the study 19 (15%) were diagnosed as GDM. The median (interquartile) of FBG was significantly higher in women with GDM [81 (70–95) vs. 67(60–75) mg/dl; P = < 0.001] compared to women without GDM. There was no significant difference in hs-CRP, serum magnesium, HOMA-IR, QUICKI and HOMA- β between women with GDM and women without GDM. No correlation was observed between body mass index (BMI), serum magnesium, hs-CRP, FBG and insulin levels. Conclusions First trimester hs-CRP and serum magnesium levels were not correlated with the later development of gestational diabetes in this setting.