Pregnant women in developing countries are vulnerable to multiple micronutrient deficiencies. Studies assessing serum levels of the micronutrients and magnitude of their deficiencies are very scarce in African subjects. This study was aimed at determining serum levels of micronutrients in 375 pregnant (42 HIV seropositive) and 76 non-pregnant women (20 HIV seropositive) who visited the University of Gondar Hospital, Gondar, Ethiopia. Serum concentrations of zinc,\ copper, selenium, calcium, and magnesium were determined using an inductively coupled plasma mass spectrometer. Irrespective of HIV serostatus, pregnant women had significantly higher serum concentrations of copper and copper/zinc ratio and significantly lower magnesium compared to those in non-pregnant women (P < 0.05). Except for selenium, which was significantly lower in HIV-seropositive pregnant women (P < 0.05), the mean serum concentrations of zinc, copper, calcium, and magnesium were not significantly different between pregnant women by HIV serostatus. The prevalence of deficiency in zinc, magnesium, selenium, and calcium in the pregnant women, irrespective of their HIV serostatus, was 66.7%, 25.6%, 21.9%, and 9.3%, respectively. The magnitude of deficiency in zinc, magnesium, and selenium was significantly higher in HIV seropositive pregnant women (76.2%, 52.4%, and 45.2%) than that in HIV-seronegative pregnant women (65.5%, 22.2%, and 18.9%) and in HIV-seronegative non-pregnant women (42.9%, 8.1%, and 30.4%; P < 0.05). Deficiency in one, two, three, or four mineral elements was observed in 44.8%, 14.4%, 9.9%, and 5.1% of the pregnant women, respectively. Only 25.9% of the pregnant women and 44.7% of the non-pregnant women were not deficient in any of the micronutrients. The high prevalence of micronutrient deficiencies in pregnant and non-pregnant women in Gondar, Ethiopia warrants the need for strategies on prevention and control of the deficiencies.