Domesday Book was commissioned by William the Conqueror (1066-1087) at Christmas 1085. It was designed to show who held every piece of land in the newly conquered Kingdom of England. It was known colloquially as the Domesday Book because it was seen as being as final as the Last Judgement and as difficult to conceal things from. The book does not cover the whole country - Cumberland, Durham, Northumberland, and Westmorland were omitted and London and Winchester likewise, along with some other towns. A separate book, called Little Domesday covered the counties of Essex, Norfolk and Suffolk and, despite its name, it is actually bigger and more detailed than the Great Domesday Book containing the other counties.

The entry for Clophill records that Nigel de Albini held the land himself, without a tenant. The manor was of five hides. It contained five villagers, five smallholders and a slave. These would all have been men, to get an idea of the total number one should probably multiply this figure by at least four, to allow for wives and children - giving a total of about 50 or so. The manor had been worth £8 in 1066 but this had fallen to 30 shillings when de Albini acquired it but had risen to 60 shillings by 1086. It is suggested by historians that the reason for the general lowering of the value of manors in the area is accounted for by William I's armies coming through Bedfordshire on their way to put down rebellions in the north. They would have lived off the land and no doubt have committed certain acts of vandalism in what was, to them, still alien, even enemy, territory.

Before the Conquest two of Earl Tostig's thegns held the manor. Tostig was the brother of King Harold and had died fighting against him at StamfordBridge in 1066 alongside King Harald of Norway.

It is interesting to note that no mill is recorded in Clophill but a mill is recorded in the next entry in the book, for Cainhoe. This, together with the reasonable size of the population of Cainhoe, larger, indeed, than Clophill, suggest that Cainhoe was then just as important, if not more so, than Clophill.