indigestion (n.)

word-forming element meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant, a tendency which began in later Latin), from Latin in- "not," cognate with Greek an-, Old English un-, all from PIE root *ne- "not."

In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.

late 14c., digestioun, "conversion of food to a state in which it can be absorbed into the blood from the alimentary canal," from Old French digestion (13c.) and directly from Latin digestionem (nominative digestio) "digestion, arrangement," noun of action from past-participle stem of digerere "to separate, divide, arrange," etymologically "to carry apart," from dis- "apart" (see dis-) + gerere "to carry" (see gest).