Kanna Haruhiko (male), for reasons unknown to him, is suddenly turned into a girl.

He returns to his male form some time afterwards, but with the continuing cycles between turning into a girl and then back to a guy, he is bewildered by the differences in both physical aspects and ways to communicate with other people.

Plus the abrupt changes that happen to his relationship with other people including his best friend and his childhood friend.

A dramatically depicted story about men and women...

Miyano Amata, known as the "Perfect Prince" for his intelligence, looks, and cool personality, is asked to substitute for his sister as an attendant at a doujinshi convention disguised as a loligothic girl. There he meets a girl from his class and they become friends, but he must crossdress in order to be with the girl while learning about the fujoshi fandom.

Notes:

? Fudanshi = BL fanboys: Some may be gay, some may be straight. More info can be found here.

? Fujoshi = (Literally) Rotten girl: A pejorative Japanese term for female fans of manga and novels that feature romantic relationships between men, often with the implication of yaoi concept.

From Viz: When schoolgirl Takiko Okuda attempts to destroy her father's translation of The Universe of the Four Gods, she is instead literally sucked into the story, becoming the Priestess of Genbu in an epic journey to find the seven Celestial Warriors!

Kouta is an ordinary high school student. He has a very feminine brother who is more like a sister. He dresses as a girl so even Kouta's friends mistake her as a girl. Kouta seems to care for his brother very much. How is their relationship going to change?

From Sura's Place:
Cha Ji-Yyoung is a journalist who makes a terrible mistake and is forced to make amends for his fault. He is forced to crossdress and enter a woman's university to reveal corruptions. His interesting life as a 22-year-old female dancing student begins.

Kuragehime follows Tsukimi Kurashita, an 18-year-old who moved from Kagoshima to Tokyo to become an illustrator. Tsukimi is a jellyfish otaku who comes to live in a shared bath and toilet, women-only apartment, Amamizukan. Other tenants include fujoshi, NEETs and others who consider fashion their natural enemy, calling themselves "Amars". One day, Tsukimi meets a fashionable and beautiful girl, Kuranosuke Koibuchi, who saves a jellyfish that is about to die at a pet shop. She later discovers that Kuranosuke is merely cross-dressing in order to evade inheritance of his father's occupation as a politician.

Note: Won the Kodansha Manga Award for best shōjo manga in 2010 and was nominated for the 2010 Manga Taishō award.

From Fallen Syndicate: "My father's last words were a curse, binding me even after his death." Genkyou is a city-state ruled by status and comprised entirely of nobles. Crime and underhanded deals seem to be an everyday occurrence and one in which many turn a blind eye. To fulfill his father's dying words, Iori travels to Genkyou determined to do whatever it takes to extract his father's revenge. However, their may be more to Iori than meets the eye.

Wataru starts his high-school life by getting forced to cross-dress by his senpai Ayane Takamura.

Compilation of the short stories:

• Family Complete
Mirin Asami and his three brothers are told by their father to cross-dress, but while Mirin's brothers enjoy dressing and acting like girls, Mirin doesn't.

• Family Compilation
This story focuses on the oldest son Momiji. Momoji Asami and his three brothers are told by their father to cross-dress, and he tries to be a perfect girl. However, this gains him unexpected attention from someone in his class.

• Family Contact
This story focuses on the youngest son Natane. The four cross-dressing Asami brothers go to the beach. The youngest runs into a classmate.

Himeno transferred to a former boys' school, Hallelujah. The president of the students association, Gao is an extreme misogynist, and the relationship between the two becomes intense.

From Viz:

Sudou Mikuzu has a very special talent--she can see ghosts. And because of this predisposition, she's become a magnet for all sorts of unwelcome monsters. Luckily for her she's just met Seto, a friendly, cross-dressing young exorcist. Sudou needs protection from all the creepy phantoms bugging her, and Seto needs to practice his exorcism skills. Consequently, the pair decides to team up and help each other. In return, Sudou promises to bake a cake every time a ghost gets zapped!

Hidaka Ikumi lost contact with his older brother Tomo at a young age after Tomo was adopted by another family. Now in present time, with Ikumi at 16 years, Tomo had suddenly returned. Much to Ikumi's surprize, Tomo had came back dressed as a woman. Or at the very least, a very girly man. What had happened to Tomo that would cause him to now dress like this and why did he return? [From ShoujoMagic]: Ikumi HIDAKA is a young man who lives with his grandmother and enjoys doing chores in his spare time. Then one day, his older brother Tomonori, whom he lost contact with when the boy was adopted by another branch of the family at the age of 5, returns. But why does Tomonori now look like a woman...!?

'S' is a known as a bully caretaker, who avenges her bullied clients -- for a price, of course.

However, in reality, 'S' is a nerd named Kang Song Ih, with a twin brother named Kang Ah Eul, whom she loves above anything. Ah Eul attends Chungha High School, a famous and expensive school, but over winter break, he attempts to commit suicide. Song Ih, determined to understand why her brother tried to kill himself, attends Chungha High School, pretending to be Ah Eul -- uncovering the reasons why Ah Eul was driven to suicide, including one mysteriously handsome but "bad" guy named Suh Ga Yoon.

Read as you follow her life while staying in an All-Boy's school and living in a dorm -- with a male roommate, who happens to be a famous singer and someone she as "S" had once nearly beat up.

Watch out! Whoever bothers "S"'s brother, prepare to face her!

Itsuki is the number one host at the club 'The Rose Garden'. Somehow, he has fallen in love with Ryou, the shy, innocent newcomer. Itsuki is unsure how to confess his feelings, but then, for the club's 5th anniversary, he is asked to wear a very special costume... Will Itsuki's beauty catch Ryou's eye?

From Seven Seas:

Being a girl is harder than it looks...
For Hazumu, this couldn't be more true, because just the other day, she...was a he.

Shunned by the girl of his dreams, Hazumu loses himself in the mountains and is promptly squashed by an oncoming space ship. The alien inside, feeling guilty, rebuilds Hazumu's body...but as the wrong gender!

Now Hazumu must learn how to be the girl his parents always wanted while dealing with the trials and tribulations of being caught in a love triangle between two girls--his childhood friend, Tomari, and Yasuna, the girl who rejected him but is now strangely attracted to him/her!

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.

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Kei Yoshikawa, a normal - if very pretty - boy in high school is one day informed that he is genetically female. The shocking relevation causes Kei to restart his life as a beautiful girl named Megumi, while keeping it all a secret from her very handsome male friends. And of course they immediately find out, but all begin hitting on her?!

Kohamaru comes from a peculiar family - each member can switch bodies with his or her soul mate! His parents can switch bodies, and his aunt, oddly enough, can switch with her cat! Now it's Kohamaru's turn...

When Kohamaru literally runs into Nanao, the girl of his dreams, they switch bodies. True love, right? Well, unfortunately, she's in love with someone else. And if that weren't bad enough, the "someone else" turns out to be Kohamaru's twin brother Konatsu... who can reverse their transformation with his own kiss!

Keidai Saeki is a high school student who remembers his past life in Pompeii, living as the Italian warrior Sirix. His friends around him are all also reincarnated - although they don't quite remember things the way he does. Keidai's wife from the past? She's now a middle school boy - while his best male friend is now a cute girl?! Throw in a case of love at first sight, and you have a new look at romance - manga-style!

From CMX:

High school student Yukari Fujimaru knows a potential star when she sees one…because she sees the special "aura" they give off, in the form of angelic wings. Yukari's fellow student, the beautiful Ryoko Katsuragi, has a small pair of wings herself, and is one of these aspiring talents. She's so talented, in fact, that no one even knows that "she" is actually a boy in disguise. Now, to make her own down-to-earth dream come true, Yukari must help her new friend become a star.

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...