Mepiquat chloride (MC) is widely used for controlling cotton plant growth. Shoot growth modifications may affect root growth and, consequently, interfere with the cotton sensitivity to water deficit. This study aimed at evaluating the water deficit effects, in initial phenological stages of cotton plants from seeds treated with MC doses, on shoot and root growth. Two experiments were carried out in a greenhouse, in Santa Helena de Goiás, Goiás State, Brazil, in a randomized blocks design, in a 4x4 factorial scheme: four growth regulator doses (0 g, 2 g, 4 g and 8 g of active ingredient of MC per kg of seed) and four water stress conditions (without water deficit and initial water deficit in three vegetative growth stages: V1, V3 and V5), with four replications. Shoot and root dry matter, as well as cotton plant height, decreased with the increase of MC doses. The water deficit between V1 and V5 reduced shoot and root dry matter. The water deficit also increased the inhibitory effect of MC applied via seeds on cotton plants shoot and root dry matter.