- Tojo wants to know whether Valmet would back him up if they were attacked by Colonel Matrix (she'd ditch him — Koko is the only one she protects). In the English version, it changes to a reference of the Agent enemies in the Matrix franchise.
- Voshkod 6 and their black tactical uniforms is a reference based on Tom Clancy's Rainbow Six series.
- During a VIP protection exercise, Tojo lands in the mud and half of his face and body was covered in mud horizontally. This leads to being called Two-Face.
- Bookman shares his background with Jack Ryan, being an Annapolis graduate who was commissioned into the US Marines, was medically retired after a severe back injury in a helicopter crash, and became a senior CIA officer.
- Kaspar's bodyguards are named Edgar, Allan and Poe.
- Before he leaves SR, Tojo angrily asks since when they became Golgo 13, infiltrating nations to conduct assassination jobs.
- Lehm nicknames one William Nelson as Wile E. Coyote due to his love of rewiring the enemy's bombs so he can blow them up in their faces, which eventually just becomes Wiley.
- Koko, Kaspar and Floyd Hekmatyar have the same family name as Gulbuddin Hekmatyar, the (in-)famous Afghan Mujahideen leader.
- Wiley takes great delight at his work (that of a slightly Mad Bomber) and even claimed to "have the spirit of a true artisan". Deidara, anyone?
- Jonah is a white-haired Child Soldier with ambiguous ethnicity. Which is the exact description of Raiden.
- After her capture Leila curses using the euphemism "frack" in a shout out to either Battlestar Galactica or Judge Dredd.
Shout Out / Jormungand