In a cramped and dirty cell, four women sit side by side on a stone bench, waiting patiently for their turn to testify in court.
The women's cell is littered with cigarette butts and pieces of tissue with lipstick marks.
In the corner, instead of a urinal, there is a female toilet, hidden by a modest wall designed to discourage peeping toms.
But among the women is a man - or certainly a person who looks like a man, judging by the way he is dressed and from his demeanour.
Alter Hofan says he is a man, but doctors say he was born a woman.
Alter is charged with falsifying his identity papers.
He was reported to police by his mother-in-law, who says he changed his gender on his birth certificate in order to marry her daughter.
But Alter says he has Klinefelter's syndrome, a male-only genetic disorder caused by the presence of an extra X chromosome. Those affected are usually infertile, and can present some female physical characteristics.
His case has highlighted the plight of the transgender community in Indonesia.
Behind bars, waiting his turn to testify, Alter seemed calm and ready to continue with his battle to live a normal life.
"I don't know what is wrong with me - this is my body, and I got this from God," he told me as I shouted out questions to him from the media scrum outside his cell.
"My wife's family - they don't want me to marry her, and it's because I'm not really perfect."
A few miles away from Alter's Jakarta cell, Hartoyo is also fighting for his right to be accepted.
A devout Muslim and a gay activist, he has suffered for his sexual orientation.
Three years ago he was living with his boyfriend in Aceh, one of Indonesia's most devoutly Islamic provinces, when a dozen people raided his house and turned the couple over to the police.
Hartoyo thought the police would protect them. Instead, the police assaulted them.
He cannot contain his emotion as he recalls what happened that night.
"I get so angry when I remember what happened," he says. "The police urinated on my head and beat the two of us up. I am still traumatised by that experience."
'No right to judge'
Aceh is one of the few provinces in Indonesia that has autonomy, and therefore is allowed to implement its own laws - specifically Sharia or Islamic law.
In September 2009, Aceh's legislative council passed a by-law that criminalised homosexuality and stipulated that adulterers be stoned to death.
This is in contrast to the rest of Indonesia, where being gay is not punishable by law.
Hartoyo was finally released from prison after a friend of his and a well-known activist intervened.
Hartoyo's experience in Aceh has not stopped him from staying true to his religion.
Most Muslims believe that Islam forbids homosexuality, but Hartoyo says he cannot stop being gay or being Muslim - and that no-one has the right to come between him and his faith.
"I believe a sin is a matter between an individual and his or her God", he tells me.
"Other people don't have the right to judge. They don't have the right to say whether or not I'm a good Muslim."
While being gay in Indonesia is not illegal, in a country that is predominantly Muslim, it is not easy.
While most Muslims practise a relatively moderate form of their religion, there are concerns about an increasing number of people joining hard-line Islamic groups.
Earlier this year, some of those groups stormed a hotel where an international gay and lesbian conference was going to be held.
Frightened about what these men might to do them, many of the attendees hid in their rooms.
Members of these Islamic groups insist they are not violent, and that all they are doing is trying to enforce Islamic values.
One of the most vocal anti-gay Muslim groups is the Islamic Defenders Front, or the FPI as it is known in Indonesia.
I met with one of the FPI's members, Munarman, who told me why he is so vehemently against homosexuality.
"Gay people are mentally ill. God didn't make them that way," he told me.
"They choose to be with people of the same sex and it is a crime in our religion. If the government doesn't want to do anything about them, we have to."
Indonesians have a reputation for tolerance.
While being gay, lesbian, bisexual or transgender in Indonesia is yet to be widely socially acceptable, many Indonesians are able to live comfortably and without prejudice - as long as they do not go out of their way to attract attention to themselves.
A proposal to criminalise homosexuality in Indonesia in 2003 failed - a sign that the majority of the country is not keen to implement strict penalties for sexual orientation.
But the concern is that elements of conservative Islam are becoming increasingly vocal in Indonesia's pluralistic society.
And this small group of hardliners could change Indonesia's image as a modern Muslim nation.