There are now many PC systems in common use that combine SCSI drives or devices with IDE/ATA ones. This is easier to do now that it has been in the past, but still takes more work than using only one or the other by itself. For the most part you end up having to do double the work since you have to configure two different interfaces. Still, there are situations where it makes sense. For example, you may want to add a SCSI optical disk or other device but continue using IDE/ATA hard disks, since they are significantly less expensive than SCSI ones. Many people also add IDE drives to existing SCSI systems to store infrequently used large files, or for backup purposes.

In most cases, IDE and SCSI devices can be combined without too much difficulty. In particular, adding non-hard-disk SCSI devices to an existing IDE/ATA system rarely poses much of a problem. The difficulties seem to be largely confined to mixing SCSI and IDE/ATA hard disks. In particular, many people who mix SCSI and IDE hard disks want to boot from the SCSI drive, because it is probably the fastest one in the system. However, by default, PCs will look for and boot the first IDE/ATA drive they see in the system, since the system BIOS natively supports IDE/ATA and not SCSI. This causes fits for people who have been using an all-SCSI system and add an IDE drive, and find the PC now wants to boot the new drive.

There are a couple of ways to get around this. The easiest one is to use a system whose BIOS supports booting from SCSI instead of IDE in a system that has both. This is typically implemented via the boot sequence BIOS setting. Today, most newer PCs will support this feature, but some retail PCs don't provide the boot sequence feature. Many older PCs don't have this setting either.

Another option is to set up your drives so that only the SCSI drive has a bootable primary partition. Configure the IDE/ATA drive to only contain logical, non-bootable volumes in the extended partition. If you do this, the system may boot from the SCSI drive because it is the only one that is bootable. Of course, if the IDE/ATA drive already has a primary partition, you will have to use a third-party repartitioning tool to change it. This also may not work on all systems or with all operating systems; the boot sequence solution is preferable.

Finally, there can be complications if you try to use a SCSI host adapter and some types of add-in IDE/ATA controllers in the same PC. IDE cards like the Promise "Ultra" series appear to the system as if they were a SCSI card. If there is also a real SCSI host adapter, which drives are recognised first comes down to which card is seen first by the operating system at boot time. If you have this configuration and the drives are being seen in the "wrong order", you may be able to fix the problem by manually changing the various cards' resource settings. Swapping the PCI slots used by the two cards may also correct the problem.