From Go! Comi: Like most teenagers, Mashiro Ichijo has a secret. But Mashiro's secret is that he’s neither fully male nor female! So far, Mashiro's been able to live his life as a boy, but all this changes when he's informed of a new class he must take in order to graduate from his elite prep school. To pass, he must find the “Key”…and the only way to find it is to enter into a nightmare world where his body and soul are put at the mercy of the worst kind of enemies: his classmates!

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Based on the Idolmaster Dearly Stars DS game. Ryou has always had a problem with his feminine appearance. As a child he was often mistaken as a girl, and to his disappointment, that didn't change even after he got to high school. One day he came up with his best idea yet for gaining masculinity; he decided to become a male idol! His cousin Ritsuko worked in the idol industry, so she was able to get him an audition. Unfortunately for his master plan, the company decided that he would make a wonderful female idol. Now, to even have a chance at becoming a male idol, he must first become successful as a girl!

Keiichirou Mishima is a 15-year-old guy living with his mom until she suddenly decides to fly to Paris to be with Keiichirou's dad. His mom arranges with his uncle Shirasaki to let him stay at his mansion with his two cousins Marie and Tomari, who he met many years before when he stayed with them for a short while. However, Keiichirou has forgotten nearly everything about back then, including why his cousins apparently now hate him.

Junichi Sasaki joins his school's drama club upon entering high school. However, he soon finds himself dressing up as a girl for his first stage performance.

The story starts off on a deserted island with a woman shouting "I ain't a chick!" while being chased by 100 male perverts in underwear!!! Then it cuts back several hours earlier and we get to see how 'she' got into this situation.

--- that is the only weapon that can oppose the mysterious life form visiting the earth. The protagonist, Kirasagi Hayato, aims to become a using this Hundred. He managed to get into the battleship university . However --- "I wanted to see you, Hayato!!!" "H-How do you know my name?" Around the roommate, Emil Crossford, who somehow knows him well (?), Hayato gets an uneasy feeling. What's more, just after the entrance ceremony, he gets asked for a duel by the campus' strongest martial arts master Claire Harvey...!? The ultimate academy battle begins here!

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!

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.

Rando Masashi, a self-centered, brash karate star, was the victim of a horrific bus accident that left him comatose, his face terribly disfigured by extensive burns. Genius plastic surgeon Dr. Manabe saved Rando's life and went to work on his face, gradually reconstructing it based on a photograph found in the wreckage of the bus. When Rando wakes up from his coma, a year has passed, and Dr. Manabe has made remarkable progress. But in a cruel twist of fate, the photo that the doctor used as his reference was not a picture of Rando, but of Rina Kurimi, the girl whom Rando has a crush on!

From Imangascans: Mahiro has two goals in life: first, to finally confess to his childhood friend who he loved for so long and second, to become a famous model. But there are various obstacles in Mahiro's path! For one thing, he dresses as a girl, named Hanabusu Arisu, when modeling. As if that wasn't enough, every woman in his vicinity gets the urge to spread her legs because of the special pheromone he emits! Will Mahiro ever come to confess his love to Miwa, or will he simply widen his harem and get engulfed in endless orgy? Find out for yourself!

Just before they enter high school, the boys Meguru and Shou are whining about the fact that neither of them has a girlfriend. A strange, large-breasted woman shows up, claiming that she will fix their problem, and kisses Meguru. This odd occurrence is pushed out of the boys' minds when they meet up with Souko, a friend from elementary school, who is going to be in their high school. She's grown up into a pretty young girl, and it seems like the boys might have a shot with her! That evening, Meguru realizes that the strange kiss may have had more meaning than he thought: he's turned into a girl! He convinces Shou and his mother of his identity, but no one has any idea how to turn him back. Now he's going to have to learn how to be a girl and let go of his hope of dating his cute childhood friend Souko. What will happen to his hopes for a popular high school life?

After losing a bet, Tao Nozomu's baseball team is forced to dress up as cheerleaders and cheer for their rivals, the Titans. However, after the bet is all settled and done, Nozomu finds he likes crossdressing almost as much as he likes baseball. Despite interior conflict with such desires, he tries to give it up; but one day, he discovers he's turned into a girl?!

From Pink Everlasting Dream Scanlations: Sakura Aki is a penniless high schooler who likes to cook and does other "unmanly" things. His grandfather and father are disciplinary on gender roles and beat up Aki everytime he does a thing that women would usually do, like cleaning. When his father leaves him absolutely broke, and with his grandfather realizing Aki's "unmanly" flaws, he sends him to live at one of the dorms at an all girls' school that he runs, a school where distinguished young ladies of the country attend, the Hanayashiki - Flower Estate-, to teach him a lesson. He meets Kitahiro Renge, a girl with un-ladylike manners and a meat loving obsession. An encounter that's going to save Aki Sakura or just another problem in sight?!

From The Pink Panzer: In the year 2999, only eleven cities still survive on Earth. The climate has changed drastically, and a biochemical apocalypse has made women extinct. For centuries, the male population of Earth has survived by depending on only one woman, called the Holy Mother, whose ova are harvested to create genetically engineered children. By now, any concept of a world in which women exist as ordinary people is long gone. Society has re-structured itself around all-male families, and gay relationships have become the norm. At the beginning of Marginal, the Holy Mother is assassinated by a terrorist known as Grinja. The government in power doesn't want to start a mass panic, so it pretends that the Holy Mother has only shed her vessel, and that she will be miraculously "reborn" in the near future. The public, which is superstitious and devout, believes this easily. Only government officials know that behind the scenes, there is a frantic effort to create a new being with an XXY chromosome -- a male capable of giving birth. (This is a BL misrepresentation of an actual phenomenon known as Klinefelter's Syndrome.) The manga's story revolves around one such boy -- Kira, the product of a genetic experiment, who becomes involved in a three-way relationship with Grinja, the aforementioned terrorist, and Ashijin, a young man who calls himself Kira's owner. A complex plot and flawless world-building make the story irresistible, and Kira's search for freedom is as symbolic as it is gripping.

Having upset the president of the student council and embarrassing her in many different situations, Tsukasa is forced to do a small "punishment" by the president. Part of Otoco Daughter Comic Anthology ~ Forced Hen ~

Oneshot from Nisioisin and Kawada Yuuya. A boy suddenly wakes up to find out he's in the body of a High School girl. Who is she and how did he switch bodies?

From Intercross: Ooji Subaru transfers from an all-girls school to a co-ed school so that she won't be away from her father. She has had recurring dreams of a beautiful and gentle princess, but she believes that this is because of her admiration of princesses. Upon entering her new school, she encounters three guys -plus her childhood friend- who claim to be...?!

Aikawa Ayumu is a normal high-school boy, until one day he is killed by a serial killer. The necromancer Eucliwood Hellscythe revives him--but as a zombie. As he begins serving Eu as her guard, he happens to deprive a mahou shoujo (magical girl) named Haruna of her magic power. Haruna orders Ayumu to take her place and fight against anti-mahou shoujo system, "Megalo." From Yen Press: Life—or undeath?—isn’t easy for Ayumu Aikawa. A seemingly normal high schooler, he is in fact a zombie who serves as a bodyguard to an introverted necromancer. But his already complicated existence becomes even more outlandish when he accidentally steals the powers of a magical girl, transforming into one himself—complete with frilly dress and pink chainsaw!! How’s a reanimated corpse supposed to keep his head on his shoulders with roommates like these girls around the house?

From Mangascreener: The main character is Leonora, the daughter of an impoverished noble of Padua. She is a beautiful silver-haired, emerald-green-eyed girl and very good at fighting with the sword. One day, she is forced to marry an arrogant young noble, but she discovers on the day of their wedding that this man intends to use her to become king of Italy because she is involved in an ancient Italian legend: Leonara is the girl shown on "Kakan no Madonna" (Madonna of the Flower Crown), a famous painting drawn by Leonardo DaVinci. There exists a legend that tells whoever gets the legendary sword "Emerald Lion" will unite and rule over Italy. And the secret hiding-place of the sword can be found with "Kakan no Madonna"--that is, Leonara. In order to find out the truth of the portrait's secret related her and to hide her identity as Kakan no Madonna, Leonara disguises herself as a black-haired boy, Leo, and sets out to find DaVinci. On the way she meets Falco, the blond-haired handsome king of Naples, who is unaware that she is a girl, and becomes his servant. When she finally finds DaVinci, she hears with surprise that she - the girl portrayed in Kakan no Madonna - is destined to possess the legendary Emerald Lion and therefore to become queen of Italy.

Assassins--they are humans that have exceptional skills which they use in killing people. The most dangerous among them is the Assassin of Crimson--the former leader of the Assassin guild Yuuyami, and the one who killed the country's leader, King Mars. Due to this, the country's princess has declared that whoever captures her will obtain fortune and become the princess' husband, essentially becoming the next king. Virgil is a guy who has red hair and looks like a girl. He is travelling with a performing troupe while searching for his twin brother Serge. His peculiar features seem to have matched the known characteristics of the Assassin of Crimson. The following events will lead him to discover the mystery behind the death of the king--and the identity of the Assassin of Crimson.

From the Ultimate Manga Guide: Fairy tale/fantasy. Lots of parody from famous fairy tales. About a girl who is raised as a boy... "good-old-days-shoujo" style art & story.

Claudine is a woman convinced since she was young that she was born into the wrong gender. She struggles through life, being the first child after three older brothers to take after their father. She wants only to be able to find true love...

A boy with female features is chosen by his drama club member to act as a fake girlfriend for their club, so they can practice on him before they actually get themselves girlfriends. This is series that started as a one shot and after a 1 1/2 year hiatus was given its very own series.