Rootstocks tolerant to iron (Fe) deficiency can be used to cope with Fe chlorosis damage. In the experiment, two peach (Prunus persica (L.) Batsch) rootstocks Garnem and GF 677 grown under Fe deficiency conditions were compared. Plants were subjected to Fe deficiency for three months, and some leaf physiological and histological responses were assessed. The relative growth rate of scion diameter and the root to shoot dry weight ratio decreased in both rootstocks. Leaf malondialdehyde content increased in rootstocks Garnem and GF 677 by 22% and 15%, respectively. In leaves, total phenolic content decreased in both rootstocks. Leaf chlorophyll and chlorophyll precursor concentrations decreased under Fe deficiency. Midrib and xylem thickness, xylem conduit width and number of xylem conduits decreased because of Fe deficiency, and the decreases in the parameters were found higher in rootstocks Garnem. Iron triggered leaf cell division, but cell expansion could not occur due to the lack of Fe. The results of the experiment demonstrated that Fe is a prerequisite for chlorophyll biosynthesis and leaf cell expansion, and GF 677 is a more tolerant rootstock to Fe deficiency compared to Garnem and can be used in peach orchards subjected to Fe deficiency conditions.