Upgraded systems do not use GUID Partition Tables (GPT), but retain the older MSDOS-based partition label.
For most ESXi 4.x hosts, the partition table is not rewritten in the upgrade to ESXi 5.x. The partition table is rewritten for systems that have lopsided bootbanks. Lopsided boot banks can occur in systems that are upgraded from ESXi 3.5 to ESXi 4.x, and then upgraded directly to ESXi 5.x.
For ESX hosts, the partitioning structure is changed to resemble that of an ESXi 4.x host. The VMFS3 partition is retained and a new MSDOS-based partition table overwrites the existing partition table.
For ESX hosts, any data stored in custom user created partitions inside the Service Console is not preserved in the migration to ESXi 5.x.
Upgraded hosts do not have a scratch partition. Instead, the scratch directory is created and accessed off of the VMFS volume. Each of the other partitions, such as the bootbanks, locker and vmkcore are identical to that of any other system.
In upgraded hosts, the VMFS partition is not upgraded from VMFS3 to VMFS5. ESXi 5.x is compatible with VMFS3 partitions. You can upgrade the partition to VMFS5 after the host is upgraded to ESXi 5.x. See the information on upgrading datastores to VMFS5 in the vSphere Storage documentation.
Upgraded hosts, which keep the older MSDOS-based partitioning, do not support installing ESXi on a single physical disk or LUN larger than 2TB. To install ESXi on a disk or LUN larger than 2TB, you must do a fresh installation.
For the VMFS partition on the disk to be preserved during an upgrade to ESXi 5.x, the partition must be physically located after the boot partition, which is partition 4, and the extended partition on the disk (8192 + 1835008 sectors). Any system that has a VMFS partition after the 1843200 sector mark can keep that VMFS partition, regardless of whether it was initially installed with ESX 3.5 or 4.x.
For systems in which the VMFS partition is placed on a different drive from the boot drive, the entire contents of the boot drive is overwritten during the upgrade. Any extra data on the disk is erased.