Although the children malnutrition in Madagascar and the environmental pollution of this country has been widely discussed, there is no research on the susceptibility of malnourished Malagasy to toxic elements. Nine elements concentration (Al, As, Cd, Cr, Hg, Ni, Pb, Sn, Sb) was determined in 103 samples of schoolgirls scalp hair (8–15 years old), and in twenty samples of water and soil, from two areas: Antananarivo (UR) and Berevo (RU). Samples were analysed by an inductively coupled plasma-optical emission spectrometer using a microwave-induced nitrogen plasma atomic emission spectrometer. The nutritional status was evaluated by Cole’s Index. The recommended level of Sb was exceeded in the soil samples, while the Al and Ni in the water. Underweight was related to higher accumulation of Al, Cd, Cr, Pb, and Ni in the hair and more common among girls living in RU than UR region (42% vs 28%). . Two-factor analysis of variance showed differences in the Al and Cr content in the girls’ hair depending both on their place of residence and nutritional status. This indicate that the malnourished girls may be more susceptible to soil and water pollution with toxic elements than girls with adequate nutritional status.