Some low-end boards have a mixture of PCIe and PCI, but new machines normally only have PCIe slots. The difference is in the number of channels for the different slots, where 16-channel slots are normally reserved for graphics cards, unless it is a high-end motherboard, in which case there are many 16-channel slots to allow the use of high-end RAID and network cards.

But just as there was a period where computers had PCI + ISA or PCI + VLB, the availability of PCIe boards have reached a critical mass, so the for the mass market, new computers don't have a need for PCI slots.