The IDE controller on your motherboard provides something called IDE/ATA channels for your devices to attach to. Each channel can support either one or two devices. IDE devices contain their own controller hardware so there must be a way to differentiate between the two devices on the channel. This is done by giving each device a designation as either master or slave, and then having the controller send commands and data to either one or the other. When a command is sent to the channel the target responds to it, the other ignores it.

Despite the sound of master and slave, both drives have the same equal status, none doesnt rely on the other for proper operation. A better naming for these would be "drive 0" and "drive 1" as used in the specifications. The only difference between master and slave is the order in which they are processed for example during initialization or when DOS assigns drive letters (Windows 2000/XP lets you change drive letters manually).

Jumpering

The selection which drive becomes master and which becomes slave is done using jumpers, these are small plastic connectors that fit over pins and form an electrically connection to "program" the drive.

If you are using two drives on a channel it is important to jumper them correctly. One drive must be master, the other slave. It does not matter which connector is used for master or slave in a standard IDE setup. However, when using Ultra DMA in a single-drive configuration you should use the end connector because of electrical signaling issues.
A single device on the channel should be jumpered as master, not as slave.
Some drives, for example made by Western Digital, have three possible jumper settings: Master, Slave, Single. Use the single setting when your drive has it and you are running it as only drive on the channel.

For performance reasons, it is better to avoid mixing slower and faster devices on the same channel. If you can, for example when you have one harddisk and one CD-ROM on a motherboard with two ide channels, give each drive its own channel. This will increase performance during concurrent accesses, for example when copying files from the CD-ROM to the harddisk, because only one device can "talk" on the channel at the same time. This also avoids issues that sometimes appear when only one of two drives on the channel is running in Ultra DMA mode.

Cable Select

An alternative to the standard master/slave jumpering system used in the most PCs is the use of the cable select setting. With this system the cable, actually the connector the device is attached to, determines which device becomes master and which device is slave. The goal of cable select is to eliminate having to set master and slave jumpers, allowing simpler configuration.

To use the cable select feature you need a special cable. Pin 28 of the IDE cable carries the CSEL signal. This signal is grounded at the motherboard side. The master connector has this pin connected so pin 28 is ground when a device is connected to it. The slave connector has an open circuit (no connection) on this pin.

When a drive is attached in cable select mode it checks pin 28 whether is it ground or not connected. If it is ground the drive sets itself to operate as master, if there is no signal it sets itself to operate as slave.

Unfortunately the cable select system was never successful because on standard IDE cables pin 28 is ground on both connectors. This was probably done to avoid extra manufacturing costs during making the cables.

Another disadvantage of cable select on 40-conductor IDE cables is that the master connector of the cable is in the middle, leaving you with a hanging stub when using only one drive. This also has electrical disadvantages.

The cable select feature was much improved with the introduction of 80-conductor Ultra DMA cables. The key changes were that the master connector has been moved to the end of the cable, putting the slave in the middle and all cables must support cable select now. You should be aware that if you swap an old 40-conductor cable select cable with an 80-conductor Ultra DMA cable your drive positions will swap logical positions, so you will have to change the order in which your drives connect to the cable.