Note that different authoritative sources list his offspring differently. The 2003 edition of Burke's (1) list the following:
whereas Anderson (2) lists:
and Hamilton (3) lists:
Hamilton argues "On 20 May 1441, Sir James of Hamilton. Kt, Lord of Cadzow. granted to his cousin, ,James of Hamilton. son of the late Walter· of Hamilton. the lands of Raploche. (Witnesses: John of Hamilton and Gawaine of Hamilton brothers of the grantor, Arthur of Hamilton. Alexander of Hamilton and Thomas of Hamilton of Neilsland. This charter indicates, by its stated relationship of Sir James Hamilton to the grantee that the founder of the Raploch branch of the family was Walter Hamilton.
In relation to his reported first son however, as a result of extensive genetic genealogy research carried out by the Hamilton Surname Project, it has now been shown that contrary to popular belief John, the 4th Baron of Cadzow cannot have been the father of James (5th Baron of Cadzow).
Genetic testing of numerous descendants of James has shown that he carried a particular genetic marker on his Y chromosome. This marker, an SNP (single nucleotide polymorphism), is designated L-1237.
Similar testing involving descendants of John (ie James' half brothers) as well as descendants of John's non-lineal ancestors (uncles etc) has indicated that all of these males carry the SNP L-338.
This is further explained in the following extract (4):
Until a few years ago it was thought that James Hamilton (the 5th of Cadzow) was the son of John Hamilton the 4th of Cadzow but through the marvels of genetic testing it is now quite clear that this just cannot be. Who the actual father was is still a mystery but his genetic “finger-print” is known and the search goes on.
Two papers have been combined into one on the Internet and are highly recommended for anyone interested in exploring this mystery. One of the papers also gives an excellent account of the politics of the time providing an essential background to the emergence of this branch of the family.
Clearly James Hamilton was not a Hamilton in terms of bloodline but then what is a “Hamilton”. The first of the line to consistently use the surname Hamilton was David Hamilton around 1381:
He was the first of the family recorded as formally using the name Hamilton, appearing in a writ of 1375 as "David de Hamylton, son and heir of David fitz Walter", in 1378 he is styled as David de Hamilton and in 1381 as David Hamilton, Lord of Cadzow. (1).
So there is the first officially recorded Hamilton of the line in 1381, only a few years before the birth of James. Prior to that surnames thought to have been used by the male line of family include de Hamilton, fitz Walter, fitz Gilbert, Beaumont, Audemar, Harcourt, Sachsen and even Frithuwald. What is important is the blood-line because at that time the legitimacy of the birth radically affected the right and ability to inherit titles and property so the subterfuge successfully conducted by Janet and her entourage has had a long lasting effect on the family and its fortunes.
What the genetics also tell us is that the father of James and his step-father (John) shared a common ancestor possibly 2,000 years ago and he lived somewhere in what is now North Western Germany.