Naruto and Naruto Shippuden, thanks to the length, are both chockfull of villains. Most of them got overshadowed by the bigger threats. By the end of Shippuden, the original Team Seven was already facing a world-ending threat from another dimension. Thus, viewers tend to forget some of the minor villains along the way who have made such a climax possible.
It's not that they weren't powerful. In fact, some of them even have the potential to be as threatening as Madara or Kaguya. The showrunners simply had other plans for them. Make no mistake though, Naruto's minor villains are definitely evil or lack some kind of morality. This led them to commit some serious crimes and these ten are the worst offenders. Do note that it's not a ranking as one can't quantify evil.
9 Kabuto
- Allegiance: Orochimaru
- First appearance: Naruto Episode #23
Kabuto Yakushi was a seemingly harmless young man who even appeared to assist Naruto and some of the Genins back in the Chunin Exam arc. However, his true colors quickly showed up as soon as his master Orochimaru started executing his plans.
While Orochimaru ultimately became irrelevant in the later seasons thanks to the introduction of newer villains, Kabuto still tried to tap into his master's essence. He also sort of became Orochimaru in a twisted way after integrating with his essence. He eventually became quite a formidable opponent and forged an identity for himself in a way.
8 Jugo
- Allegiance: Orochimaru
- First Appearance: Naruto Shippūden Episode #116
Jugo was one of Orochimaru's and later Sasuke's pet projects and he actually came to Orochimaru hoping for a cure for his violent urges and uncontrollable rage. Because there were times when Jugo would become berserk and "accidentally" destroy villages and murder its inhabitants.
He is aware of his disposition yet doesn't seem too remorseful about it. If anything, he treats it more like an annoyance. Regardless, he still pledged allegiance to Orochimaru and became an instrument for him, carrying out his experiments and morally dubious plans.
7 Kimimaro
- Allegiance: Orochimaru
- First Appearance: Naruto Episode #118
Kimimaro was one of the rarest descendants of the Kaguya Clan who possesses immense power exclusive to their bloodline. As such, he was treated as a weapon for most of his life where he was locked up and only brought out in fights. Orochimaru eventually recruited him as one of his most loyal ninjas and his twisted philosophies and goals eventually brushed off on Kimimaro.
This resulted in Kimimaro fighting for Orochimaru with unbelievable loyalty. Even an insult in passing to his master is considered a major offense. At times, Kimimaro's evil is almost instinctive as he more or less has no free will and acts more like a loose cannon who needs a target.
6 Deidara
- Allegiance: Akatsuki
- First Appearance: Naruto Shippūden Episode #2
Deidara was one of the first unique ninjas introduced at the start of the Shippuden time jump. He was one of the members of the Akatsuki and was tasked with assaulting the nation of Suna at the start of the season. What makes him rather evil is that he's blindly obsessed with his art.
He makes explosives designed as origami pieces and typically cares for nothing else. He only wants to see the results of his art regardless of whether they cause havoc or death for the beholders. For this, he's easily one of the most twisted members of the rogue ninja faction.
5 Kakuzu
- Allegiance: Akatsuki
- First Appearance: Naruto Shippūden Episode #71
Most of the members of the Akatsuki are either deranged or mad with power but many of them would still want to avoid partnership with Kakuzu. This Akatsuki member is infamous in his group for killing four of his teammates and then consuming their hearts to fuel his power. He did it because he has a short fuse.
Someone that unstable and prone to wanton murder is one of the most basic definitions of evil. Kakuzu has no regard for human life and is easily angered, making him more like a rabid dog with no restraint nor composure. It doesn't help that he toys with his victims' corpses afterward.
4 Hidan
- Allegiance: Akatsuki
- First Appearance: Naruto Shippūden Episode #71
At first glance, Hidan seems like one of the more collected and reasonable Akatsuki members. He even claimed to be religious. However, he's quite a hypocrite has one of the most profane vocabularies out of all the Akatsuki. He also regularly insults his peers and complains about them.
As for how evil he is, Hidan is similar to Kakuzu who seeks to pioneer immortality. He even actively seeks out evil places whom he deems might help with his personal goals. He also has no moral restraints and would hesitate on killing any citizen if it helped his rituals.
3 Sasori
- Allegiance: Akatsuki
- First Appearance: Naruto Shippūden Episode #2
Sasori was partnered with Deidara during the Akatsuki's assault on Suna and the two of them made quite a formidable team. He's an expert in puppetry and utilizes puppets and several types of poison in order to slowly kill and torture his opponents. In his preferred manner of dispatching his opponents, one can easily see Sasori's morals or lack thereof.
Personality-wise, he's similar yet conflicting with Deidara. Both of them consider themselves artists but Sasori believes that his art should be permanent and makes it a habit to make everlasting puppets out of his victims. To that end, "dying" to Sasori in combat isn't a relieving experience.
2 Kisame
- Allegiance: Akatsuki
- First Appearance: Naruto Episode #80
Compared to other Akatsuki members, Kisame looks rather tame with his sword and water jutsu skills but he's still a ferocious fighter who sates his bloodlust with constant fighting. Kisame will actively seek out opponents just to feed his monster sword.
He's also inherently sadistic and even suggested dismembering hostages in order to transport them easier. Even before he joined the Akatsuki, Kisame already has a warped idea of honor as he killed his own master after learning to be a legendary swordsman.
1 Kurama
- Allegiance: Naruto (eventually)
- First Appearance: Naruto Episode #1
It's hard to pin where Kurama stands since he later became an anti-hero and one of Naruto's closest friends but for most of Naruto and even in Shippuden, Kurama's an evil demon who would have become a major villain if only he were free from his shackles.
Being a Chakra Monster, Kurama is destined to be a destructive force of nature and even came close to wiping out Konoha before Naruto's timeline. Even as he was imprisoned inside Naruto, he remained quite an uncontrollable menace and was only brought to heel a little too late.