This was a daring construction, contrary to normal Roman practice (which favored extra-thick walls) and to basic concepts of engineering. The Renaissance architect Leon Battista Alberti severely criticized the design around the middle of the fifteenth century, when he found the upper walls leaning out of plumb; but by then they were already 1100 years old.
Windows in the outer aisle walls filtered light into the nave, but the principal natural illumination came from the nave clerestory: eleven windows on each side, piercing the wall above the colonnade. Theoretically eleven windows could have been aligned with alternate intercolumniations [with 22 columns, there were 23 intercolumniations], but it is not certain that this was so. If not, fenestration and colonnades followed two slightly different rhythms in the nave. There were also a number of windows in the walls of the transept.
The reconstruction of ceilings and roofs remains uncertain. Two texts from around 400 use the term lacunar, which means coffered ceiling, with reference to the transept (and nave?), but if such a ceiling existed it was forgotten by the later middle ages. The south-north section made around 1608 by Grimaldi shows open timber roofs over the nave and aisles.
If such a roof was visible originally, its beams would have been gilded. Since the span of the nave was more than 87 ft. (ca. 23.6 m.), those beams there were enormous. Pope Honorius I had to replace 16 of them in the seventh century, and the new beams were gilded as well. The same pope received permission from the emperor to take bronze roof tiles from the Temple of Venus and Rome in the Roman Forum to put on the roof of St. Peter's. Over the aisles, the 17th-century section shows a single continuous roof; if this is accepted as the original arrangement, one has to explain the purpose of the semi-circular openings in the inner aisle walls. For this reason some scholars prefer to reconstruct a stepped profile, with the roof over the outer aisles about 18 ft. lower than the one over the inner aisles, and the openings functioning as windows between them.
The height of the transept also is not known for certain; many scholars believe that it was not as tall as the nave.