From MangaHelpers: Muto Yuzuki was ready for a whole new life and a different self when she got to middle school but she didn't expect it to be literally torturous. Yuzuki is “persuaded” by an upper classman named Funaki Aoi to join the Torture Club on campus which has been secretly training students to enter the field of military and police organizations as interrogation experts. Aoi sees something inside Yuzuki and thinks she might be a prodigy in torture methods. Naturally, Yuzuki wants nothing to do with such vulgar conduct but the more she spends time with the club, the more she starts to realize her own dark potential. [vyc]

Masato Kataoka moves into his new dorm to begin his life in high school when one day, a cute girl named Yuki Nomura becomes his roomate. Masato learns that Yuki is an old childhood friend, but becomes surprised when he realizes that Yuki was, and still is a guy. Yuki's charm and affection for cross-dressing leaves Masato with feelings of discomfort and fright. Find out how Masato manages to deal with a cute cross-dresser and the many obstacles of high school life. Résumé by: Krasae

A boy wants to confess his love to his senpai, but his plans are ruined when he turns into a girl. The twist is when she finds out that he's a girl, and she tells him she used to be a boy too, and promises to show him the ropes of girlhood.

This series follows the adventures of two main characters as one of the characters goes through a series of episodes in discovering his female identity as a trap. This is a series in which each adventure is a self encapsulated oneshot not dependent on previous oneshots for a coherent understanding of a story to occur.

This is a wonderful tale set in historical times that deals with amazing legends... A strong and active young boy named Duo Xi and a gentle young girl named Xiao Que live in a village at the base of a mountain which, legend has it, is home to female fox demons. Among the foxes is the very special Cai Sheng--a little girl fox with the power to one day become what only the most powerful foxes can become: a man, able to sire celestial fox children. Lonely, with no one her age to play with, the child fox Cai Sheng descends to the village and plays with Duo Xi and Xiao Que, and when the little fox child is attacked by a dog, it's the two human children who save her! Now the humans are marked, and will remain so--even in their lives to come--until Cai Sheng repays her debt to them... Two hundred years later, Cai Sheng is more powerful and has mastered the art of becoming a man...and she still owes a debt to the reincarnated children! -- ShoujoMagic (Clarifying note: Very low ecchi content)

Eruna was entrusted with ruling a country at a very young age when her father, the king of a small kingdom, fell very ill. With such a heavy burden placed upon a mere teenager, the king gave Eruna an important piece of advice about how he made his time of rule a success: find your shadow. By finding her double, she will find the will to live and be brave even in the most dire situations. Eruna does find a person who looks identical to her but it turns out fate loves to play games. Teshio used to be a simple rancher who had a problem of always being mistaken for a girl but he is about to go from rags to riches because he becomes the new shadow for princess Eruna.

Merleawe has left her hometown and moved to the capital city of Viegald to attend wizarding school. On her way to her first day of school, she bumps into a man who kidnaps her and takes her to the castle, where she is charged with an awesome task”impersonating the kingdom's master wizard! Fearing war would break out if it was known the master wizard, Sylthfarn, was missing, Sylthfarn's inner circle has decided someone must pretend to be him. Merleawe tells them that she will take the job! But not only does she lack the ability to cast more than simple magic, she also has no idea who the master wizard was! Unraveling the twisted threads of Sylthfarn's disappearance and keeping up the appearances of both master wizard and first year wizarding student makes Merleawe's every day challenging, magical, and amazing!

The life of daimyo Uesugi Kenshin commanded authority and fear during the Sengoku period of Japanese history. In this retelling, the powerful lord is reimagined as a woman.

Living in regret that his formula gave birth to the atomic bomb, Professor Einstein sends two boys whose eyes can see the future on a train that travels at the speed of light before embarking on his own final adventure: death. His hope is that they will find "HER" and tell her his wish, for it is only she who can grant it. Fifty years later, it is 2005 and the place is Tokyo. At last, "SHE" (Ruika) has been found... but Ruika has an unusual circumstance. For her mother's sake, she's been living as her dead brother since childhood. Does Ruika truly have the power to grant wishes? If she grants her mother's wish by becoming a boy, then no one can lead us into the GLOBAL GARDEN... Now it's a race against time and against each other, because everyone has a dark past and an ulterior motive for possessing the girl who can grant Einstein's wish.

Kei is a normal--if very pretty--young boy in high school. One day, he falls ill and is taken to the hospital. They find, much to everyone's surprise, that "he" actually has a female genotype even though "his" phenotype is male!! A little bit of surgical work solves the problem, and cool male hero Kei becomes innocent female heroine Kei. And what a female! "He" was cute before, but she is a beauty now.

Sequel to Mai Otome.

From Wikipedia: Hanabuki High School prohibits its pupils from wearing makeup. Among the school girls there is a rumour going around about a legendary make-up artist, Ageha, who secretly gives makeovers to girls after school. Any girl wanting Ageha to give them a makeover needs only to write their name and class on Ageha's card (showing Ageha's trademark, a swallowtail butterfly—agehach? in Japanese) and put it up on the school's notice board, and Ageha will later show up in their classroom. However, no one knows that Ageha's true identity is the quiet, bespectacled girl, Rin Fujiwara, except for the play boy, Riku Kisaragi. Amused by the idea, Kisaragi cross-dresses as Ageha's assistant to tag along with her as she works. A running gag in the story is that Ageha's clients think that Kisaragi is Ageha upon first meeting.

From ShoujoMagic: Hatori is a tall girl who's easily mistaken for a boy, and she's in love with her childhood friend, Keishi. Even though he's a boy, Keishi is so cute that Hatori just wants to push him down and make him her own. Hatori has countless delusions and hallucinations (unbefitting a young lady) running wildly through her head every day -- and they're all about Keishi. They set her heart pounding and her nose bleeding!

Tayutama Kiss on my Deity centers on Yuuri Mito, a student at the Sousei Academy and the only son of the man who runs the Yachimata shrine. At Yachimata, there is a legend of a deity named Tayutayu-sama who protected the area, but this deity and other so-called “Tayutai” have been lost in time. Mito and his friends discover a relic on the school grounds with mysterious patterns on them. Then, at the opening ceremony of the new school year, an equally mysterious girl named Mashiro appears before Mito. Mashiro is somehow tied to the relic and the legend of Tayutayu-sama… [Mangaupdates]

From Wonderland After Hours: Atsuko is a young high-school girl who leads a troublesome life. Working a scandalous job for the sake of survival, her reputation is in tatters and she is scorned by her peers. But one day she is noticed by one of three rich boys, Itaru, which she resembles in an uncanny way. Immediately she finds herself whisked away from her everyday life and into a new world where she is forced to take on the role as Itaru's double and replace him as the "Prince".

One day, ordinary junior high schooler Shirahime Kanata is forced by his mother, Konata to sign a contract that transforms him into a "magic girl" in times of trouble. As a magical girl herself, Konata wants to pass her job onto her son so he can protect the peace while she goes on vacation. Unfortunately for Kanata, canceling the contract means he'll permanently change into a girl, so now he's stuck doing an embarassing job. Along with the help of his supervisor, a perverted cat named Moel, Kanata will fight against the "Noise," magical enemies who try to disturb the peace...all while wearing a cute skirt!

This is a story about a mob ojisan who, one day, suddenly becomes the heroine of an otome game. TL/N: Mob in this case means NPC instead of gangster

From Impossibility: Morisawa Kai and Sato Tatsuki are best friends. However, unlike Kai, Tatsuki is completely unreliable, lazy and ill-tempered. One day Tatsuki takes Kai out driving in his new motocycle only to get into a bad accident that leaves Kai dead. However, Kai's spirit ends up in a body of a girl named Fujii Marika. After seeing how cold and unaffected Tatsuki as well as everyone else was after his death, Kai transfers to his previous school in which he starts noticing flaws to Tatsuki's cool mask...

Short Program is a collection of short stories compiled 4 volumes. The stories are all unrelated and vary in length and genre, from Shonen, Shojo, Seinen, and Josei. Many of the stories were previously published as one-shots in various manga magazines, the earliest being from 1978. Release Dates: Short Program Vol.1 - November 1988 Short Program Vol.2: -June 1996 Short Program Vol.3: - July 2007 Short Program: Girl's Type - May 2009

From Omari's Sister: Yukari, at the tender age of 17, is a renown Edo period novelist who claims visions of Yoshihara during the Edo period gush from his heart. After meeting Mahoro, a girl he swears he knows and has met before, Yukari finds himself falling asleep and waking up in the Edo period as an Oiran. The past and present collide in this time traveling romance.

Kaguya is a boy in an all-girls' school for demons [fox spirits, succubi, werewolves, etc]. Being the only human is bad enough, but the added risk of his manhood being discovered makes for silly and unbelievable (deliciously enviable) situations.

From Operation Boredom: “'I’ll create a witch!!” During the 17th century, the German alchemist Johann Schultz successfully created a witch. He then injected that power into his own blood. In the present day, as a result of a scheme created by his cousin, Yomoda Rena, Shurutsu Kenichi, a high school student and a third generation German, fights on secretly as a blood relative of "Brocken", all in order to hunt down those who abuse the artificial witch theorem. Yet for reasons unknown, he transforms into a Magical Girl "Heroine"...? A series from the mangaka of Übel Blatt!!

From Tokyopop: Inez is a young orphan girl with a special gift that allows her to communicate with all creatures. A great destiny awaits her, the nature of which she is yet unaware. As our story opens, Inez is traveling with an old wizard named Kaager and a faithful dog named Zode. Her country is about to plunge into its first winter in one hundred years and ominous signs abound concerning the return of a demon-race which threatens the country's fragile peace. Can little Inez- via a magic amulet - bring back her country's ancient dragon protector in time?

Yashi has wandered with her father for fourteen years, and only now has she discovered that her own mother is actually Bocinia’s current queen. To see her mother, from whom she was separated when she was just an infant, she and her father enter the palace, but she never thought she would accidentally run into the Princess of Bocinia, and then become her bodyguard by mistake...