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The Pinacoteca section of the Vatican Museums is where the paintings are. As one might expect, the Vatican has amassed a formidable collection of religiously-themed paintings over the centuries, and many noteworthy works are on display in the Pinacoteca. Here are a few:
Last Judgment
Last Judgment, Nicolaus and Johannes (12th C.)
Stefaneschi Triptych/Coronation/Madonna
Stefaneschi Triptych/Coronation/Madonna

Musical Angels
Musical Angels, Melozzo da Forli (ca. 1480)
Musical Angels
Musical Angels, Melozzo da Forli (c. 1480)

Pieta
Pieta, Lucas Cranach the Elder (16th C.)
Altarpieces and Paintings
Altarpieces and Paintings

Rospigliosi Triptych
Rospigliosi Triptych, Bartolomeo da Foligno (15th C.)
Assumption of the Virgin
Assumption of the Virgin, Niccola Filotesio (1515)

Madonna and Child with Saints
Madonna and Child with Saints, Pietro Perugino (1495)
Nativity/Madonna and Child with Saints
Nativity/Madonna and Child with Saints

Madonna di Foligno
Madonna di Foligno, Raphael (1511-12)
Nativity
Nativity, Ghirlandaio (15th C.)

Lament Over the Dead Christ
Lament Over the Dead Christ, Giovanni Bellini (1473-76)
The Savior/Adoration of the Magi
The Savior/Adoration of the Magi

Adoration of the Magi
Adoration of the Magi, Raffaellino del Colle (16th C.)
Vision of St. Helen
Vision of St. Helen, Paolo Veronese (c. 1580)

Judith with the Head of Holofernes
Judith with the Head of Holofernes, Cristofano Allori(?) (17th C.)
Deposition from the Cross
Deposition from the Cross, Caravaggio (1600)

Crucifixion of St. Peter
Crucifixion of St. Peter, Guido Reni (1604)
Apotheosis of Vincenzo I Gonzaga
Apotheosis of Vincenzo I Gonzaga, Peter Paul Rubens (School) (17th C.)

St. Ignatius of Loyola
St. Ignatius of Loyola, Seghers and Wildens (1622-23)
St. Francis Xavier
St. Francis Xavier, Seghers and Wildens (1622-23)

Adam and Eve in the Garden of Eden
Adam and Eve in the Garden of Eden, Peter Wenzel (18th C.)

Among the Renaissance paintings is the almost-finished Transfiguration by Raphael (1517-20). Raphael was something of a party animal, and was apparently taken ill following a particularly disgraceful night of carousing in 1520. He was placed under the care of some of the finest medical minds in 1520 Rome and consequently did not survive. The Transfiguration was found in his workshop, and was displayed at his funeral. It is considered to be his last painting.
Transfiguration
Transfiguration, Raphael (1517-20)
Transfiguration and Crowning of the Virgin
Transfiguration and Crowning of the Virgin

Crowning of the Virgin
Crowning of the Virgin (Oddi Altarpiece), Raphael (1502-03)

Less finished is St. Jerome in the Wilderness, by Leonardo da Vinci (ca. 1480-82). Though the painting never got very far in its development, it shows Leonardo's talents for composition and anatomical accuracy, and is also interesting as a window into his creative process.
St. Jerome in the Wilderness
St. Jerome in the Wilderness, Leonardo da Vinci (ca. 1480-82)

See the next page for some old stuff, from ancient Rome and earlier.