The main objective of this work was to compare the tolerance to lime-induced Fe deficiency of two lines of Medicago ciliaris (TN11.11 and TN8.7). We studied the effects of Fe deficiency on:(1) root biomass and rhizosphere acidification, (2) accumulation in the roots and the exudation into the rhizosphere of organic compounds (citric acid, malic acid and phenols), (3) changes under Fe deficient conditions in the activities of two enzymes, the first related to organic acid metabolism (malate dehydrogenase: MDH) and the other to proton extrusion (H + -ATPase activity). After a pre-treatment of one week, plants were transferred into hydroponic culture under three treatments: +Fe, −Fe and +Fe +lime. Iron deficiency led to 40% increase in root biomass in TN11.11 line in the presence of lime. Both the omission of Fe and the addition of lime to the nutrient solution increased the H + -ATPase activity more in TN11.11 than in TN8.7. In addition, Fe deficiency increased accumulation of organic acids as well as phenols in roots, and stimulated the MDH activity more in TN11.11 than in TN8.7 (+75% and +41% in TN11.11 and TN8.7, respectively). Iron deficiency also increased the amounts of citrate, malate and phenols in root exudates. Our data allowed us to note that the TN11.11 line is more effective in overcoming Fe deficiency than TN8.7.