A USB MIDI card plugs into a USB port on the exterior of your computer's case. A PCI card, on the other hand, slides into a PCI slot on the motherboard inside the case. USB MIDI cards are much easier to install; setting up a USB MIDI card simply involves plugging it in, then possibly running a driver utility. To install a PCI MIDI card, however, you must open your computer's case, then install the card in its slot on the motherboard.
PCI is much faster than USB. The common USB 2.0 standard supports a maximum transfer speed of 480 megabits per second, while even the slowest PCI connections can transfer information at speeds of up to 133 megabytes -- 1,064 megabits -- per second. This faster transfer speed reduces the influence of MIDI latency, which can cause delays when recording from an external MIDI device onto the computer. These delays, however, are measured in milliseconds, and may be so short as to be unnoticeable to your ears.
One of the great advantages of a USB MIDI interface is its high level of portability. If, like many electronic musicians, you use a desktop for production and a laptop for live performances, you can simply unplug the USB MIDI card from your desktop, take it to a gig, then plug it into your laptop. A PCI MIDI card, on the other hand, is more or less permanently installed on your desktop.
Keep the hardware requirements of the two interfaces in mind when you're deciding whether to purchase a USB or PCI MIDI card. When you plug a USB MIDI card into a USB port on your system, you lose the use of that port, and can no longer connect an external hard drive, for example, to the port. PCI slots are also limited: if you have several PCI cards already installed on your system, there may be no space for another PCI card. Additionally, USB MIDI cards may require an external power supply -- although some can draw power from the USB port -- while PCI cards are powered by your computer's power supply.