Ferdinand's Vault holds Sophie in the below Southeast pier along with others. Her Parents are buried in Franz Joseph's Vault. For a listing of the layout and the burial places of the various Hapsburg's see below link:
By 1908 the seven vaults of the crypt already held 129 bodies, plus the heart urns of another 3 persons. In that year the Franz Josephs Gruft was built, along with the adjacent Chapel, as part of the celebrations of Emperor Franz Josef's142 60 years on the throne. The vault is usually entered from the north wall in the rear, through the southeast door of the New Vault.
From the foot of the tombs, left to right:
Franz Joseph's Vault, showing the pedestal of the stone tomb of Emperor Franz Josef, flanked by wife Elisabeth and son Rudolf.
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143 Empress Elisabeth of Bavaria ("Sissi") (1837 - 1898) →Family Tree Wife of Emperor Franz Joseph.142
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142 Emperor Franz Josef (1830 - 1916) →Family Tree Son of Archduke Franz Karl.135
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144 Archduke Rudolf (1858 - 1889) →Family Tree Son of Emperor Franz Joseph.142
Turning around from the foot of the tombs, the doorway on the south wall of this vault leads into the Crypt Chapel.
Ferdinand's Vault
The Ferdinandsgruft was built in 1842, along with the Tuscan Vault, in conjunction with the reconstruction of the monastery above. Although the visitor sees an almost-empty room with only two sarcophagi, this vault actually contains one-fourth of the Imperial Crypt's entire population, walled-up into the corner piers.
Within the southeast pier:
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73 Archduchess Maria Antonia (1858 - 1883) →Family Tree Daughter of Grand Duke Ferdinand IV of Tuscany.108 Died at 25.
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74 Archduchess Maria Anna (1835 - 1840) →Family Tree Daughter of Archduke Franz Karl135 and Sophie of Bavaria,137 sister of Emperor Franz Joseph142 Died at 5.
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75 Archduchess Maria Karolina (1821 - 1844) →Family Tree Daughter of Archduke Rainerx783 and Princess Elisabeth of Savoy. Died at 23.
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76 Archduke Ferdinand Salvator (1888 - 1891) →Family Tree Son of Archduke Karl Salvator90 and Maria Immakulata.89 Died at 3.
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77 Archduke Rainer Salvator (1880 - 1889) →Family Tree Son of Archduke Karl Salvator90 and Maria Immakulata.89 Died at 9.
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78 Archduchess Sophie Friederike (1855 - 1857) →Family Tree Daughter of Emperor Franz Joseph142 and Empress Elisabeth (Sisi)143 Died at 2.
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79 Archduchess Karoline Ferdinanda (1793 - 1802) →Family Tree Daughter of Ferdinand III, Grand Duke of Tuscanyx769 and Luisa Maria Amelia Teresa of Naples.84a Died at 9. Her heart is buried in the Herzgruft in the Augustinerkirche.
http://en.wikipedia.org/wiki/Imperial_Crypt_Vaults