PCI Express connects graphics cards, NVMe drives and expansion cards to the rest of the system. The version numbers and lane counts matter less than their prominence suggests, with a few specific exceptions worth knowing.
Lanes and versions
A lane is a serial connection. Devices use a number of lanes, written as x1, x4, x8 or x16. More lanes means more bandwidth.
Each PCIe version roughly doubles the bandwidth per lane over the previous one. A PCIe 4.0 x8 connection carries about the same as PCIe 3.0 x16.
Slots are backwards and forwards compatible. A PCIe 4.0 card works in a PCIe 3.0 slot at the older speed, and vice versa. Nothing breaks; the connection simply runs at whatever both ends support.
When it actually matters
For most graphics cards, very little. A card using x16 at PCIe 4.0 loses a small amount of performance in a PCIe 3.0 slot, usually low single-digit percentages.
The exception is cards that use only eight lanes electrically, which several mid-range models do. In a PCIe 3.0 board, an x8 card gets half the bandwidth of x16, and that can be measurable in some titles. Worth checking if you are putting a new mid-range card into an older board.
For NVMe drives it matters even less in practice, because everyday use is dominated by small random reads rather than sequential transfers that saturate the link.
Lane budgets and shared slots
A processor provides a fixed number of lanes, and the chipset provides more. There are not enough for everything at full width simultaneously.
This is why populating a second or third M.2 slot commonly disables SATA ports, and why adding a card to a lower slot can drop the graphics card from x16 to x8.
The board manual documents which combinations conflict. It is worth reading before buying storage or expansion cards, rather than after.
Physical size and electrical width are different
A slot can be physically x16 while only wired for four lanes. This catches people out because the card fits perfectly and simply runs slower than expected.
Board specifications usually write this as something like “PCIe x16 slot (runs at x4)”. The lower slots on consumer boards are frequently wired this way, because the processor lanes are reserved for the primary slot.
Slots may also be open ended, meaning a physically larger card can be inserted into a shorter slot with the end hanging out. This works electrically, at the narrower width.
The practical consequence: if you move a graphics card to a lower slot to make room for something, check what that slot is actually wired for first.
How to check what you are actually getting
Monitoring tools report the link width and generation currently negotiated, usually shown as something like “x16 4.0”.
Worth checking after building, because a card not fully seated frequently negotiates a narrower link rather than failing outright. A graphics card reporting x8 in a slot that should give x16 is usually seated slightly crooked.
Cards also drop to a lower generation at idle to save power and raise it under load. A reading of x16 1.1 while the desktop is idle is normal, not a fault. Check it during a demanding game rather than at rest.