Fifteen discrete cranial variations were studied in Ainu and a number of populations from around the world. The major findings, extracted by B-squared distance analysis and Fisher's exact probability test, are as follows: A) The five key traits which distinguish Ainu from the predominant eastern Asians are (1) medial palatine canal, (2) hypoglossal canal bridging, (3) supraorbital foramen, (4) transverse zygomatic suture vestige, and (5) mylohyoid bridging. The frequency of the first trait is comparable to those of Africans, especially Subsaharan Africans, the second and fifth conform to those of the New World peoples, the third is similar to Australians and Subsaharan Africans, and the fourth is the only one aligning the Ainu to Northeast Asians. B) The frequencies of a few wormian bones in Ainu are significantly different from those of many Southeast Asians. The frequencies favour rough clinality from the south to as far north as the arctic area of Northeast Asia in the regions of western Oceania and eastern Asia. The present study confirms that Ainu and Jomon are certainly members of populations originated in Asia but possibly outliers of more predominant Asian populations.