SIESTA uses pseudopotentials to represent the electron-ion interaction (as do most plane-wave codes and in contrast to so-called "all-electron" programs). In particular, the pseudopotentials are of the "norm-conserving" kind.
The released versions of SIESTA use pseudopotential files in the 'Froyen' (psf) format. These pseudopotentials can be generated and tested by a number of programs:
Until recently the SIESTA distribution included the ATOM program, but it is no longer bundled due to licensing issues. If you are an academic user, you can download it from here.
For non-academic users, or for those looking for more pseudopotential options, we recommend a visit to the Virtual Vault for Pseudopotentials. Use one of the pseudopotential generators listed as providing psf output compatible with Siesta (such as APE) and follow the proper procedures for testing.
Remember that all pseudopotentials should be thoroughly tested before using them. (See the standard literature on pseudopotentials and the user manuals for ATOM and other generation codes for more information on testing).
In contrast, curated pseudopotential databases offer a higher level of testing and quality assurance. For example, the PseudoDojo is an open source project for developing and systematically testing pseudopotentials. These are generated with the multi-projector norm-conserving generator ONCVPSP, tested with seven different batteries of tests with ABINIT, and made available in a web-based database in several formats.
Users of SIESTA willing to try these pseudopotentials can use an experimental but soon to be merged version of SIESTA with support for the new PSML format.