- Background The Bedouin-Arab population in Israel comprises a low socio-economic society in transition. Smoking among males and consanguineous marriages are frequent. A previous study showed elevated rates of major malformations within groups from this population residing near an industrial park, where high ambient values of arsenic (As) and nickel (Ni) were detected, compared to groups living in remote localities. Objectives We estimated the extent of exposure to metals in pregnant Bedouin-Arab women in relation to congenital malformations. Methods We collected maternal urine samples from 140 Bedouin women who gave birth in a local hospital. Patient medical history, type of marriage (consanguineous or non-consanguineous), and parental exposure history were collected by interview and medical records. Results Aluminum (Al) was detected in 37 women (26.4%), cadmium (Cd) in 2 (1.4%), As in 10 (7.1%), and Ni in 1 woman (0.7%). The detected rate of Cd exposure was low, though more than 92% of the fathers reported smoking. Concentrations of Al were higher for women residing within 10 km of the local industrial park (Prevalence Ratio (PR) = 1.12, p-value = 0.012) or who reported using a wood burning stove (PR = 1.37, p-value = 0.011) and cooking over an open fire (PR = 1.16, p-value = 0.076). Exposure to Al was adversely associated with minor anomalies (OR = 3.8, p-value = 0.046) after adjusting for history of abortions (OR = 6.1, p-value = 0.007). Fetuses prenatally exposed to As were born prematurely (p-value = 0.001) and at lower weights (pv = 0.023). Conclusions The study population of pregnant women is exposed to high levels of metals mainly of household origin. Our findings may be generalized to similar populations in developing countries.