Rune slots with grey backgrounds are unavailable. Those with rune names have those runes locked into place. White slots with numbers are the levels at which those slots are gained; blank white slots are available from when the character is level 1.

Character	H	Rh	Lh
Ace		Double Tusk	32
Aila
Alanis	53		32
Augustine		Red Rose	44
Ayame		Shrike	46
Bazba		Cyclone	57
Beecham			45
Belle		37	Comet
Borus
Bright	Spreading Flame	55
Cecile		War Horse
Chris		30*	Phoenix
Connie	45
Duke			32
Dupa		Fury
Edge			43
Elaine			27
Emily		25	Haziness
Estella	20	Rage	45
Franz			56
Fred
Fubar	Shining Wind Rune	30
Futch			37
Gadget Z		Gadget
Gau		Counter	40
Geddoe	35	True Lightning*
Hallec	Wrath
Hugo		35*
Jacques		Boranda Hawk	40
Jimba
Joker	55	Isshin
Juan		17	Waking
Kenji	Full Moon	40
Kogoro			44
Koichi		38
Koroku		40
Kosanji		47
Landis		Drain	42
Leo			30
Lilly			30
Luc		True Wind
Lucia	50
Lulu			35
Mel	40	Devil's Doll	28
Melville		27	39
Mua			36
Nash			40
Nei	45	32
Nicolas
Percival
Piccolo	40		Mallet
Queen		27	Ripple
Reed		35
Rhett		53
Rico			45
Rody	40
Roland		40
Ruby	Shining Wing		44
Salome	50		32
Samus			15
Sanae Y		Sickle-Weasel	36
Sarah	Flowing
Sasarai		True Earth*	Flowing
Sergeant Joe		25
Shabon	50	37
Sharon			48
Shiba		Warrior
Thomas			32
Toppo			40
Twaikin			Warrior
Viki	45	Blinking	35
Viki (young)	45	Blinking	35
Wan Fu		32
Watari	37
Wilder		49
Yuber	45		Eight Devil
Yuiri	50		Killer
Yumi	50		Great Hawk

* Chris and Hugo gain different True Runes (which one is dependent on your decision) at a specific point in the story. The runes equipped on their RHs prior to that will be placed back in the inventory. Before that point, and in the short time where they lose their True Runes (this part also applies to Geddoe and Sasarai), the rune slot will be open, or if they have not yet reached the level indicated in the box, will have no available rune slot.