qualm (n.) Look up qualm at Dictionary.com
Old English cwealm (West Saxon) "death, disaster, plague," utcualm (Anglian) "utter destruction," related to cwellan "to kill," cwelan "to die" (see quell). Sense softened to "feeling of faintness" 1520s; meaning "uneasiness, doubt" is from 1550s; that of "scruple of conscience" is 1640s.

A direct connection between the Old English and modern senses is wanting, but it is nonetheless plausible, via the notion of "fit of sickness." The other suggested etymology, less satisfying, is from Dutch kwalm "steam, vapor, mist," which also may be ultimately from the same Germanic root as quell.