The functional movement screen (FMS) was developed as an evaluation tool for assessing the fundamental movement patterns believed to be prerequisites for functional activity. However, some of the FMS component movements, such as the deep overhead squat test (DST), likely represent novel motor challenges on which poor performance might reflect inexperience with the task rather than a movement impairment. The purpose of this study was to examine the effects of positional variations on DST scores in a population of young, healthy adults. We hypothesized that self-selecting foot positioning, removal of an overhead component, or changing both aspects of the DST would result in improvement in FMS scores. Twenty healthy subjects completed 4 squatting conditions in a counterbalanced sequence to eliminate carry over effects: DST, modified squat with hands at chest level and feet in the DST position (DSTO), modified squat with arms in the DST position and self-selected foot placement (DSTF), and modified squat with hands at chest level and self-selected foot placement (DSTB). A Friedman's analysis of variance and Wilcoxon signed-ranks' post hoc analysis revealed a significant difference between all squat conditions (p = 0.036), between DSTB-DST groups (p < 0.001), DSTO-DST groups (p = 0.004), and DSTO-DSTB groups (p = 0.046). Each modified squat condition had an average score higher than the DST. These findings suggest that the FMS DST might underestimate an individual's ability to squat during functional tasks that involve self-selected foot and arm placement.