The McQuillan DNA Project accepts any of the known spellings of the McQuillan surname:
| MacQuillan | MacQuilland | MacQuillen | MacQuillian | MacQuillin | MacQuillion | |
| MacQuillon | MacQuilly | MacWillie | McQueelan | McQueelin | McQuelan | |
| McQueland | McQuelian | McQuelin | McQuellan | McQuelland | McQuellin | |
| McQuill | McQuillan | McQuilland | McQuillen | McQuillian | McQuillin | |
| McQuillion | McQuillon | Quillan | Quillen | Quillin |
The following surnames are usually distinct clan names, but can occasionally represent a "hidden" derivation from a McQuillan surname. Thus, while these names are not considered primary variants of the project surnames, they can be accepted into the project under appropriate circumstances:
| Campbell | Cullen | Killen | MacAilan | MacCaillan | MacCaillion | |
| MacCullen | MacKillan | MacKillian | MacKillon | McAilin | McAyland | |
| McKillan | McKillin | McKillion | McKillon | McWilliam | McWilliams | |