Devices, instruments, assemblies, and systems for holding and inserting staples and staples for compressing bones or bone fragments. The staple insertion assembly including a staple holder and a staple. The staple holder including a first and second end with a gripping portion at the first end, at least one slot extending from second end toward first end, and a receiving portion at the second end. The receiving portion with at least one staple contact portion, a first recessed region positioned adjacent to the at least one staple contact portion on a first side and a second recessed region positioned adjacent to the at least one staple contact portion on a second side, and a first engagement member positioned adjacent to the first recessed region and a second engagement member positioned adjacent to the second recessed region. Methods for using the assemblies to compress bones or bone fragments are also disclosed.