"moral misgiving, pang of conscience," late 14c., from Old French scrupule (14c.), from Latin scrupulus "uneasiness, anxiety, pricking of conscience," literally "small sharp stone," diminutive of scrupus "sharp stone or pebble," used figuratively by Cicero for a cause of uneasiness or anxiety, probably from the notion of having a pebble in one's shoe. The word in the more literal Latin sense of "small unit of weight or measurement" is attested in English from late 14c.
"to have or make scruples," 1620s, from scruple (n.). Related: Scrupled; scrupling.