| Paintings | - Adoration of the Magi (Athens, c. 1565–1567)
- Dormition of the Virgin (1565–1566)
- Healing of the Man Born Blind
- Modena Triptych (1567–1569)
- Baptism of Christ (Heraklion, 1567–1569)
- Last Supper (1568)
- Flight into Egypt (1570)
- Annunciation
- Purification of the Temple
- The Fable (1570–1575)
- Entombment of Christ (1570–1576)
- El Soplón (1571–1572)
- Pietà (1571–1576)
- Penitent Magdalene (1576–1578)
- Saint Sebastian (1576–1579)
- Santo Domingo el Antiguo Altarpiece (1577)
- Saint Lawrence's Vision of the Madonna and Child (1577)
- Adoration of the Holy Name of Jesus (1577–1579) (preparatory sketch)
- Assumption of the Virgin (1577–1579)
- Disrobing of Christ (El Expolio) (1577–1579)
- Holy Trinity (c. 1577–1579)
- Saint Anthony of Padua (1580)
- Christ Carrying the Cross
- The Martyrdom of Saint Maurice (1580–1582)
- The Tears of Saint Peter
- Barnard Castle, 1580–1589
- Mexico City, 1587–1596
- Oslo, c. 1590
- San Diego, c. 1590–1595
- Sitges, c. 1595–1600
- Toledo, El Greco Museum, c. 1595–1600
- Washington, c. 1600–1605
- Toledo, Lerma Museum Foundation, c. 1605–1610
- Toledo Cathedral, 1620–1630
- The Immaculate Conception with Saint John the Evangelist (c. 1585)
- Saint Francis Receiving the Stigmata (Baltimore, c. 1585)
- The Burial of the Count of Orgaz (1586)
- Holy Family (1586–1588)
- Holy Face of Jesus (1586–1595)
- Saint Peter and Saint Paul
- Agony in the Garden
- Christ on the Cross Adored by Two Donors (c. 1590)
- Saint Louis (1592–1595)
- Virgin Mary (Mater Dolorosa) (c. 1594–1604)
- Holy Family (c. 1595)
- Christ Taking Leave of his Mother (1595)
- Saint Andrew and Saint Francis (1595–1598)
- Saint Francis Receiving the Stigmata (Pau, before 1595)
- Adoration of the Shepherds
- Doña María de Aragón Altarpiece (1596–1599)
- View of Toledo (1596–1600)
- Baptism of Christ (Rome, 1596–1600)
- Virgin Mary (1597)
- Saint Martin and the Beggar (1597–1599)
- The Virgin of Charity (1597–1603)
- Allegory of the Camaldolese Order (c. 1597)
- Saint John the Baptist (1597–1607)
- Saint John the Evangelist and Saint Francis (c. 1600)
- Saint Bernardino of Siena (1603)
- Nativity (1603–1605)
- Coronation of the Virgin (1603–1605)
- Marriage of the Virgin (1603–1607)
- Saint John the Evangelist (c. 1605)
- The Apparition of the Virgin to Saint Hyacinth (c. 1605–1610)
- The Immaculate Conception (1607–1613)
- Saint Peter (1608)
- View and Plan of Toledo (1608)
- Concert of Angels (1608)
- The Saviour (1608–1614)
- Saint Thomas the Apostle (1608–1614)
- Opening of the Fifth Seal (1608–1614)
- Saint Jerome (1609)
- Saint Ildefonsus (1609)
- Saint Francis and Brother Leo (1609)
- Saint James the Great (1610)
- Saint Luke (1610–1614)
- Laocoön (1610–1614)
- Saint Paul (1610–1614)
- Saint Sebastian (c.1610–1614)
- Saint Sebastian (1610–1614)
- Julián Romero and Saint Julian (1612–1614)
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