It is well known that in the Soviet Union there were never any independent non-governmental organizations or opposition movements. Keeping this in mind, it is clear why the observance of internationally recognized human rights norms is surrounded by controversy in present day Azerbaijan.

There are currently about 700 political prisoners in Azerbaijan. Those who can be categorized as political prisoners include:

Politicians, even if they were accused in non-political actions. For example, several politicians were falsely accused of financial violations.

People that were accused of actions against the President and his regime.

Prisoners of conscience, persecuted because of religion, ethnicity, and/or ideas.

The relatives of arrested politicians.

Political arrests have been a part of independent Azerbaijan virtually from the start. When the Soviet Union collapsed in 1991, Azerbaijan found itself engaged in a conflict with Armenia over control of Nagorno-Karabakh, an enclave within Azerbaijani territory inhabited mostly by ethnic Armenians.

At the time, when Azerbaijan was led by President Ayaz Mutalibov, there were relatively few political prisoners. For example, political activists Neymat Panakhov and Abil Huseynov, who both espoused radical nationalist ideas, were arrested and imprisoned for about one year.

In February 1992, Azerbaijan began to experience political upheaval brought on by a series of battlefield disasters in Karabakh. A massacre in the city of Hojali sparked mass demonstrations by The Popular Front of Azerbaijan. Ultimately, Mutalibov was forced to resign, and in May, the Popular Front, Azerbaijan's first democratically oriented movement, came to power.

In a sort of paradox, immediately following the rise of the new regime, the number of political arrests increased. The Popular Front-led Ministry of Internal Affairs began arresting soldiers and volunteers that chose not to participate in military battles. Officials also gave orders to arrest activists of national minorities and citizens of Armenian origin, with the intention of exchanging these citizens for prisoners from the Nagorno-Karabakh conflict that were of Azerbaijan origin.

In June 1993, the Popular Front was ousted from power in a coup led by the Commandant of the Military Unit from Ganja, Suret Huseynov. This paved the way for the return to power of the current president, Heydar Aliev. Soon after he gained the presidency, political arrests became a regular occurrence. Even Suret Huseynov himself was arrested, along with close friends and relatives, who were all falsely accused of planning a coup against Aliev. Among other prominent figures placed under arrest was Rahim Gaziyev, former Minister of Defense during the Popular Front regime, who was taken into custody in August 1995. He was accused of high treason in regards to Azerbaijan's defeats in Karabakh. Two of Rahim's brothers were also arrested. All of the aforementioned people remain in prison to this day.

Another notorious event occurred in March 1995, when members of special police units attempted a coup against President Aliev. All special police officers were accused of attempting the coup, even though only about 200 participated in the uprising. Of the approximately 1,000 special police officers originally detained, about 500 remain in custody. Up to 300 were released shortly after their arrests, some paid bribes to obtain their freedom, and others were released under an amnesty.

Among other massive arrests, there is the case of the "Generals" and the case of the "Twenty-ones". These cases were interesting because of two subjects: some of the accused people were recognized as prisoners of conscience; two of the prisoners of conscience were Rasim Agayev and Talat Najafaliyev. They were researching the idea of one mutual Eurasia space, but were accused of acting against the government. Also, during these inquiries, investigators at the Ministry of National Security started, for the first time, engaging in torture.

Political prisoners are subject to numerous human rights violations while in custody. Unlawful methods employed by officials include torture, threats, and delayed correspondence between relatives. As a result, the guilty and non-guilty remain in prison.