The museum's primary collections are those of the Habsburgs, particularly from the portrait and armour collections of Ferdinand of Tirol, the collections of Emperor Rudolph II (the largest part of which is, however, scattered), and the collection of paintings of Archduke Leopold Wilhelm, of which his Italian paintings were first documented in the Theatrum Pictorium.

Notable works in the picture gallery include:

• Jan van Eyck: Portrait of Cardinal Niccolò Albergati (c. 1431)

• Antonello da Messina: San Cassiano Altarpiece (1475–1476)

• Raphael:

  • Madonna of the Meadow (1506)

  • St Margaret and the Dragon (1518)

• Albrecht Dürer:

  • Avarice (1507)

  • Adoration of the Trinity (1511)

• Titian:

  • The Bravo (1516–17)

  • Portrait of Isabella d'Este (1534–36)

• Lorenzo Lotto: Madonna and Child with Saint Catherine and Saint James (c.1527)

• Tintoretto: Susanna and the Elders (1555–56)

• Pieter Brueghel the Elder:

  • The Fight Between Carnival and Lent (1559)

  • Children's Games (1560)

  • The Tower of Babel (1563)

  • The Procession to Calvary (1564)

  • The Gloomy Day (February - March) (1565)

  • The Return of the Herd (October - November) (1565)

  • The Hunters in the Snow (December - January) (1565)

  • The Peasant and the Nest Robber (Bauer und Vogeldieb), 1568

  • The Peasant Wedding (1568/69)

  • The Peasant Dance (1568/69)

• Giuseppe Arcimboldo:

  • The Four Seasons

    • Summer (1563)

• Michelangelo Merisi da Caravaggio:

  • The Crowning with Thorns (c. 1602–04)

  • Madonna of the Rosary (1606–07)

  • David with the Head of Goliath

• Peter Paul Rubens:

  • Miracles of St. Francis Xavier

  • Angelica and the Hermit (1626–28)

  • Ildefonso Altarpiece (1630–32)

  • Self-Portrait (1638–39)

  • The Fur (1638)

• Rembrandt: Self Portrait (1652)

• Johannes Vermeer: The Art of Painting (1665–66)

• Diego Velázquez: Several portraits of the Spanish royal family, a branch of the Habsburg, sent to Vienna.

• Thomas Gainsborough: Landscape in Suffolk (1748; currently not on display)

The collections of the Kunsthistorisches Museum:

• Egyptian and Near Eastern Collection

• Collection of Greek and Roman Antiquities

• Collection of Sculpture and Decorative Arts

• Coin Cabinet

• Library