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1550s, "to collect in heaps," variant of clotern "to form clots, to heap on" (c.1400); related to clot (n.). Sense of "to litter" is first recorded 1660s. Related: Cluttered; cluttering.
1570s, "things lying in heaps or confusion," from clutter (v.); the "litter" sense is from 1660s.