The remains of three skeletons were found inside Rosslyn Chapel when work to the heating system required floor slabs to be lifted.
Radiocarbon dating of two of the skeletons indicates they could have been buried in the mid-15th Century.
They were possibly buried at about the same time the chapel was constructed.
It is thought the skeletons were male and that at least one of them had undertaken heavy or repeated physical activity, with well-developed bone surfaces at the sites of muscle insertions.
Bones that had previously been disturbed were also found in the chapel precinct, with these dated back to between the 15th and 17th centuries. These were thought to be the remains of an adult male.
The AOC Archaeology Group in Midlothian carried out the excavation and analysis of the bones for the Rosslyn Chapel Trust, with the bones then prepared for reburial in line with guidance from Historic Environment Scotland.
Lindsay Dunbar, fieldwork project manager at AOC Archaeology Group, said: "Opportunities to work at such a world-famous and iconic monument as Rosslyn Chapel come along rarely, so it was with great anticipation that AOC undertook the archaeological monitoring during the construction of the new visitor centre and works at the chapel.
"The discovery of both disturbed and in situ burials was especially exciting given the limited amount of excavation necessary within the chapel to complete the conservation works.
"AOC was allowed ample time to complete the full excavation of the burials and the good preservation of the human bone allowed full osteoarchaeological analysis to be completed.
"Whilst it is unlikely that the burials represent the clergy, it is clear that to occupy such a space within such a small chapel means that these burials are of people important to the chapel."
Ian Gardner, director of the Rosslyn Chapel Trust, said: "The analysis provides valuable information about the age of the remains but, inevitably, questions remain unanswered about the identity of these men and their roles here.
"Today's ceremony to reinter the remains was simple but a very fitting way to return them to Rosslyn Chapel."
The Rosslyn Chapel featured in Dan Brown's best-selling novel The Da Vinci Code.
Human remains discovered during maintenance work at a historic church in Midlothian have been reburied in its grounds.