Media for the Atari usually have a root sector in the old MBR format. Up to 4 partitions are defined in the root sector, all other definitions are distributed across the disk in special structures. This format is described in the AHDI specification. DOS and Windows handle the MBR scheme in a similar way, but the MBR partition table is structured differently than in TOS, which causes compatibility issues.

With a GUID partition table, all partition data (usually for up to 128 partitions) are located on the first sectors. The last sectors always contain a complete backup of this table. The integrity of the partition data is secured by checksums. Media with a capacity of more than 2 TiB absolutely require a GPT scheme, since an MBR (like TOS) is limited to 32 bit sector numbers. 64 bit sector numbers on the Atari are supported in conjunction with the SCSI Driver by tools such as HDDRUTIL or DISKUS. The actual partition data do not change with a GPT scheme, only the structure of the partition table.
With the Atari, it depends on the hard disk software whether a GPT scheme can be used. HDDRIVER has supported GPTs since version 10.10, HDDRUTIL since version 12.50.

The Atari also benefits from a GPT scheme. The main advantages and disadvantages for the Atari are summarized below.

• Generally improved compatibility with other platforms, since the structure of the partition table is identical on all platforms. Media without FAT16 partitions do not require a special TOS/Windows format. Therefore HDDRUTIL only creates such a format if it is required.
• GPTs significantly improve the compatibility of TOS/Windows compatible partitions starting with Linux kernel 6.0.
• Linux recognizes TOS partitions without special kernel configuration and without the use of TOS/Windows compatible partitions. TOS partitions can therefore be mounted directly. With FAT16 filesystems Linux supports up to 4096 bytes per logical sector, which means that Linux can mount TOS partitions up to 256 MiB.
• Partitions of different operating systems can coexist independently of each other. Unknown partition types are ignored.
• Checksums ensure the integrity of the partition data. This allows HDDRUTIL to detect corrupted GPT data.
• Increased data security through a backup of the partition table. HDDRUTIL can restore the table, even for other platforms.
• More transparent partition parameters due to the elimination of all legacy data.
• Tools for other platforms can, like HDDRUTIL, repair a GPT for the Atari and vice versa.
• HDDRIVER detects from the GPT attributes whether a Windows or TOS partition is read-only or hidden.

• On the Atari, currently only HDDRIVER supports the GPT scheme.
• Low-level disk tools for the Atari (e.g. DISKUS) for special root sector operations only support the MBR scheme. However, such operations are better covered by HDDRUTIL anyway.

HDDRIVER users should not only consider using a GPT scheme for data exchange with other platforms. The higher data security (recovering the partition table) alone can speak in favor of a GPT scheme.

MBR partition types on the Atari consist of three characters, usually uppercase. On DOS/Windows each MBR type consists of one byte. GPT partition types are represented by a 16-byte platform independent unique ID. Therefore TOS and DOS/Windows partitions can coexist on the same medium. GUIDs are mapped to the types used on the Atari as follows.

If possible, for XHDI types HDDRIVER uses the TOS types instead of the equivalent DOS types.
When partitioning with a GPT scheme, HDDRUTIL automatically creates the corresponding GPT types instead of the MBR types, so that the user does not have to rethink. Partitioning is done as usual, and the familiar MBR types always appear externally. There are no other visible changes during normal operation either.