1540s, from Latin segregatus, past participle of segregare "set apart, lay aside; isolate; divide," literally "separate from the flock," from *se gregare, from se "apart from" (see secret (n.)) + grege, ablative of grex "herd, flock" (from PIE root *ger- "to gather").
Originally often with reference to the religious notion of separating the flock of the godly from sinners. In modern social context, "to force or enforce racial separation and exclusion," 1908. Related: Segregated; segregating.