Stephan Letter, 27, who has been nicknamed the "Angel of Death" by the German press, admitted killing some of the patients and asked their relatives for forgiveness.
"I want to confess my guilt," he told the court in the southern town of Kempten, adding that he brought his victims' lives to "an artificial end" before they could die of their illnesses.
With his head bowed, the baby-faced nurse added that nothing could justify what he had done.
Mr Letter refused to say for how many of the deaths he accepted responsibility and retracted statements made to the police after his arrest in 2004 in which he confessed to killing 12 of the deceased by lethal injection.
Denies murders
"I confessed to killings which I did not commit," he said. Mr Letter is being charged with 16 counts of murder, 12 of manslaughter and one of killing on demand.
On Tuesday he asked the court to convert all the murder charges to that of manslaughter, which carries a maximum sentence in Germany of 15 years in prison.
He reiterated an earlier claim that he had killed out of compassion to spare his patients further suffering.
But state prosecutors say Letter maliciously killed patients who were recovering and preparing to leave a clinic in nearby Sonthofen where he worked for 17 months.
The 29 patients all died during that period after being injected with a lethal combination of drugs, according to the state. The eldest was 95 and the youngest only 40 but most were in their seventies.
The deaths initially raised no suspicion, but Letter was arrested for stealing medicine from the clinic and almost immediately confessed to having killed patients.
Investigators subsequently dug up 42 graves of people who died at the clinic in Sonthofen for autopsies, in some cases amid fierce resistance by their loved ones.
Mr Letter on Tuesday claimed however that if he initially confessed to crimes he "did not commit", he had done so to prevent further graves being dug up to spare the feelings of the deceased's relatives.
"To prevent exhumations was a central motive of my confessions," he said. Sons, daughters, grandchildren and spouses of the victims filled a row of seats in the packed court room on Tuesday.
Victims angry
Nina Wagner, whose grandmother was among the 29 victims, angrily rejected Mr Letter's testimony as "cold and calculated." "It is a joke. It is so humiliating for us relatives."
Her mother added: "I want this to be over soon. I cannot describe what it feels like to sit across the room from him."
One of the main witnesses for the state is a 24-year-old soldier who says she lost consciousness after Mr Letter injected her against her will while she was in the clinic. She says she demanded a blood test and an investigation but the clinic refused.
The case has shocked Germany, and press reports have looked into Mr Letter's childhood in speculation about what may have driven him to take patients' lives.
Der Spiegel news magazine wrote that he suffered from a severe lack of affection from a cold mother who had feared that her son would be born handicapped.
Though this was not the case, she routinely subjected him to doctor's visits and painful treatment and placed him in a school for the handicapped.
Germany has seen a spate of cases in which clinic workers are charged with killing people in their care, adding to a long-running debate in the country about the state of the public health system.
Mr Letter's trial is expected to run until March.