In Bashar al-Assad's Syria, it is not just forbidden to speak, demonstrate and protest: it is also forbidden both to give medical treatment, and to receive treatment yourself. Since the beginning of the uprising, the regime has been waging a merciless war against any individual or institution capable of bringing medical aid to the victims of repression. "It's very dangerous to be a doctor or a pharmacist," a pharmacist from the Baba Amro neighbourhood of Homs tells me. Medical personnel are imprisoned – like the nurse in the nearby district of al-Qusayr, arrested the day after he showed me around his hidden emergency-care centre, its carpets covered with plastic tarpaulins to protect them from blood – or killed, like Abdur Rahim Amir, the only doctor in that centre, murdered in cold blood in November by military security, while he sought to treat civilians wounded during the army's assault on Rastan to the north. Or tortured.

In Baba Amro, a nurse from the Homs National Hospital, imprisoned in September, describes the tortures he was subjected to by miming them: he was beaten with a club, blindfolded, whipped, suffered electric shocks, and hanged from the wall by a single wrist, on tiptoe, for four or five hours – a common practice that has its own name, ash-shabah. "I was lucky, they didn't treat me so badly," he insists. "They didn't break my bones." Sometimes, the regime's forces just insult them. A Red Crescent nurse, in her ambulance, was stopped at a checkpoint: "We shoot them, and you save them!" the soldiers berated them.

The two city hospitals, the civilian (called the "National") and the military one, are under the thumb of the security forces, and their rooms and basements have been turned into torture chambers. The private clinics, last resort for the wounded of the insurrection, are subjected to permanent assault. In one, in the heart of the old city, two nurses show me the impact of bullets in the windows, walls and beds, fired by the army from the nearby citadel. Aside from these two nurses, the clinic is empty. "We can only accept emergency cases and we don't keep anyone for more than a few hours. The security forces come here regularly and arrest everyone they find. The doctors have had to sign a pledge not to take care of demonstrators."

As they speak, a bullet slaps into the room next to ours. Everyone laughs. "Ever since the Free Syrian Army (FSA) established itself in the neighbourhood," continues one of the nurses, "the wounded can be brought here." The rebel army also transports doctors for operations, when it's possible. Five days earlier, the clinic received a man with his belly torn open: a first surgeon was able to operate, but needed a specialist to complete the procedure. The neighbourhood, however, was sealed off, making it impossible to bring the specialist in and impossible to transfer the patient to another hospital. "In the end he died," concludes the nurse.

Abu Hamzeh, a highly trained surgeon, tries to care for the wounded who arrive daily at an emergency first aid point in the city. He is so desperate about the lack of resources – his centre has no anaesthetics, no medical imaging equipment, he can't operate on anyone, just bandage them and give them saline drips – that he wants to give up medicine and take up arms. "I'm useless here," he mutters bitterly in front of a man with his abdomen perforated by a sniper bullet, "completely useless." When the uprising first began, Abu Hamzeh was working at the Homs military hospital, and he witnessed the tortures inflicted on wounded demonstrators, sometimes even by nurses or doctors, whose names he carefully recorded. When the head doctor of the hospital tried to forbid such practices, they simply became more discreet. "One day, I treated a patient in the emergency room. The next day he was sent to the CT room for a brain trauma he didn't have the previous day. That's how I discovered that they did things to him at night. After two days the patient died from his brain trauma. He would not have died from the injuries I treated the first day."

Horrified, Abu Hamzeh managed to procure a camera-pen in Beirut, and secretly recorded, with the help of a nurse, four short videos in a post-operative care room. In the clips you can see five patients, completely or nearly naked beneath the sheets, blindfolded, one ankle chained to the bed. The doctor's hand uncovers their bodies: two of them bear large fresh red marks on the torso, the result of flogging. Lying on a table are the torture instruments: two supple whips, rubber straps cut out from tyres and reinforced with duct tape, and an electric cable with a plug on one end and a clamp on the other, to be attached to the fingers, feet or penis. One of the injured men groans incessantly. "They had blocked their catheters," Abu Hamzeh exclaims. "When I came in they begged for something to drink. I opened the catheters and changed the urine bags, which were full, but two of the patients went into a coma because of kidney failure. When I changed their bandages, I noticed gangrene on one of the patients; I told this to the orthopaedic section but wasn't able to follow up. Three days later I heard they had cut his leg off above the knee."

Abu Hamzeh, who recently resigned his position in order to join the opposition, was quickly sidelined. But the practices he describes have only intensified over the past months. In Baba Amro, we are taken to meet R, a wounded man whose leg has been amputated, and who was just released from the military hospital. In late December a shell fell in his street, killing five of his neighbours and relatives. In the little video they show me, you can see R bundled into a vehicle, his leg half-torn off, just held in place by a hastily tied scarf. The first private clinic where he was brought was overwhelmed with wounded, and they tried to transfer him to another one, along with his 28-year-old nephew, whose left arm was attached by nothing more than a few scraps of flesh. But the ambulance transporting them was intercepted at a security forces checkpoint, where the two wounded men were arrested, placed in an armoured vehicle, and taken to the military hospital. There, without receiving any medical attention, handcuffed to their beds and blindfolded, they were tortured for eight hours. "They hit me with food trays, on my head and body. They tied ropes to my wounded leg and pulled in all directions. They did many other things to me, but I don't remember them."

The men torturing him weren't even trying to get information, they just insulted their victims: "Ah, you want freedom, well here's your freedom!" His nephew died from the torture; finally, R was transferred to the operating room for surgery. Afterwards, he was imprisoned, without any post-operative follow-up: his leg got infected, and six days later it was summarily amputated by a military doctor. I am shown a picture of him upon his release: his skin sallow, his cheeks sunk, skeletal, but softly glad to be alive. "They killed me, back there," he concludes, his eyes shining. "I should never have come out alive."

Such practices are in no way isolated cases, individual initiatives fuelled by sadism or overzealousness, outside of any control. On the contrary, they are codified and regulated by a set of procedures far older than the current uprising, as Abu Salim, a military doctor who served for two years in the mukhabarat, the Department of Military Intelligence, before defecting to the opposition to run a makeshift clinic in Homs, testifies: "What is the mission of a mukhabarat medical doctor?" he calmly asks as my tape recorder runs. "I will explain it to you. Firstly: to keep alive the people subjected to torture so that they can be interrogated for as long as possible. Secondly: in case the person being interrogated loses consciousness, to attend to him so that the interrogation can continue. Thirdly: to supervise the use of psychotropic drugs during the interrogation. We used chlorpromazine [an anti-psychotic drug prescribed, usually, for schizophrenia], valium, and rubbing alcohol – for instance, by pouring a litre into the nose, or else by subcutaneous injection. Fourthly: if the person being tortured has reached his threshold of resistance and is in danger of death, the doctor can request his hospitalisation. However, the doctor cannot make the decision: he must write a report and the officer in charge of the interrogation then decides whether or not to grant the transfer. Before the revolution, almost everyone was transferred; now, it's only the important prisoners. The others are left to die."

• First published in Le Monde. Translated by Charlotte Mandell. (c) Jonathan Littell.

• Tomorrow: How Assad's regime is inflicting a brutal collective punishment on the civilians of Homs

This article was amended on 21 February 2012. Information that was inconsistent with Guardian editorial guidelines has been removed.