Constantinople was the successor of Rome, and the Byzantines continued the use of the old imperial 'single-headed' eagle motif. Although the roots of the transformation to double-headed are almost certainly connected with old depictions in Asia Minor, the details of its adoption are uncertain. Beyond any doubt, it was used in the wider area during the first centuries AD and certainly before the 10th century AD, as it appears in Persian and Armenian art. According to the most prevalent theory, the imperial Roman single-headed eagle was modified to double-headed by emperor Isaakios Komnenos being influenced from local traditions about such a beast (the haga) in his native Paphlagonia in Asia Minor. Local legends talked about this giant eagle with two heads that could easily hold a bull in its claws; the haga was seen as a representation of power, and people would often "call" it for protection. Isaakios Komnenos, deeply influenced by these beliefs, had already used it as a family emblem (N. Zapheiriou, "the Greek Flag from Antiquity to present", Athens, 1947). As there has been reference to "stone representations" of the eagle that were the inspiration for its picture, it is reasonable to assume that Hittite carvings may have been the sources of the myths themselves, but other relevant artwork cannot be excluded as such a source. Whether the eagle became an "imperial" symbol or remained purely a personal symbol for Komnenos, is not clear.

After the Latin conquest of Constantinople in 1204, it was used by the successor states of Epirus and Nicaea. The first mention of a double-headed eagle in the West dates from 1250 in a roll of arms of Matthew of Paris for Emperor Friedrich II. Theodore II Laskaris chose it for his symbol as Emperor (Empire of Nicaea), taking it to symbolize his state's claims to all the Byzantine Empire's former domains, both European (West) and Asian (East). An alternative (and probably more correct) interpretation is that the eagle symbolized the Emperor's double temporal and spiritual sovereignty. After the recapture of Constantinople and the restoration of the Byzantine Empire, the symbol was used as an emblem of the imperial family, but it is uncertain whether it was the official emblem of the Empire. More recent research has suggested that it was not, its usage being limited to imperial seals and other personal or dynasty symbols such as imperial robes, although there has been no depiction of any Emperor wearing it. The role of "state" symbols was most probably played by flags with the cross. In Byzantine usage, the eagle was almost always connected with colors of imperial power (gold and red). A black eagle on golden background was used outside the imperial family, denoting the subordinate position (the eagle was black as being the 'shadow' of the Emperor's golden eagle) of their bearers.

The Double-Headed Eagle of Lagash is used as emblem by the Scottish Rite of Freemasonry*. While there are many meanings attached to this symbol, * the famed Masonic author M. P. Hall declares it an alchemical symbol of union between the masculine and feminine principles in the individual.