Answer:  

It has both, but the likelihood is that the name came to Scotland via Ireland. The earliest recorded instance of the name in Scotland is in 1296 "Macrath ap Molegan of Wyggetone" in south-east Scotland.

The Gaelic form of the name is 'Maolagan' (in Old Irish 'Mael ecan') meaning 'the little bald or shaven one' which may have referred to the tonsure of the Celtic monks. 

Variations of the name 'Milligan' are: Milliken, Millikin, Millican, Mullikin.

 

 

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