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Salinity affects extensive arid and semiarid areas all over the world, producing diminished yields of many crops. Even though there is a variety of research and reviews related to physiological and anatomical modifications produced in salinity-tolerant species, today there are different points of view in relation to this topic, and especially due to technical limitations, there are few articles in which anatomical modifications have been quantified. The aim of this research is to quantitatively and statistically evaluate the modifications that are produced in radicles and hypocotyles of cotton seedlings growing in NaCl concentrations that affect the early ontogenetic stages of this crop. Germination of two varieties of cotton at increasing concentrations (0 to 450 meq/l) of NaCl was studied as well as the growth of seedlings after their germination in water. Anatomical modifications induced in radicles and hypocotyles were analyzed quantitatively with an image analyzer. There were no differences among varieties. While the percentage of germination decreased at the 252 meq/l NaCl level, the velocity of the process and seedling growth was inhibited at lower concentrations. With increased salinity, the cortex and pith of radicle increased in width, while the xylem decreased. In the hypocotyl, the width of cortex increased, as did the number and diameter of gossypol glands. This change deserves further studies in relation to the participation of these glands in the capacity of the seedlings to tolerate salinity.