When it comes to Protocol Compas specifically, Dr. Ana Maria Marchesse of Eva Peron Children's Hospital is one of several Argentine doctors who is highly critical of the study's methodology.
She heads up the Health Professionals' Labor Association, a group of local doctors who alerted La Federacion de Profesionals de la Salud de la Republica Argentina (the Argentinean FDA) of their concerns about possible wrongdoing.
"It's impossible to say whether the 12 babies' deaths are due to the vaccine or not, because half of the [total number of] children were given a placebo," the pediatrician told ABCNews.com through a translator. "But the way the study has been conducted is reprehensible."
A large part of the problem lies in the consent form, says Marchese. The language in the 12-page document is so convoluted, she charges, that even she had to read it more than once to fully grasp its meaning. Another problem is how subjects say they were recruited, Marchese says.
Claudia Nazarena Hoyos, 31, and Alvaro Martin Ovejero, 32, spoke to ABCNews.com in Ovejero's father's kitchen.
Hoyos and Ovejero allege that a Protocol Compas nurse's aide told them that 4-month-old Gabriel, who suffered from bronchial trouble, would probably get better if they allowed him to be a part of the study. Instead, Gabriel died two months after receiving his first injection.
Ovejero, who works as a part-time disc jockey, alleges the couple was misled by the "agente saniterio," a kind of nurse's aide, who told them about the study. "She did not say it was a test. She said it was a vaccine for his lungs that would keep him from getting worse."
One week after the baby received his first injection, says Hoyos, her son began to produce a lot of mucus. His eyes were perpetually runny, and his breathing grew slow and labored.
GlaxoSmithKline denies allegations of ethical misconduct. Ruttiman says the deaths have been analyzed, and says all of them were clearly unrelated to the vaccine. One child died in a choking incident, he says.
"GSK is saddened to hear of any mortality in clinical trials. Safety of patients is always our primary concern in the development of any new treatment or vaccine," Alspach said. "It is, however, important to review such cases in the context of the rates of post-neonatal infant mortality for the country in which the trial is being conducted."
Nevertheless, Ovejero insists that "something in the process was bad," and that his family and the other affected families "want to find out who or what is responsible."
Global health advocates say bad press is making it difficult for doctors working with children in the developing world, even when the doctors have no connection to clinical studies.
The Nigerian state of Kano is one well-publicized example. In 2004, Kano's government refused to take part in the Global Polio Eradication Initiative sponsored by the World Health Organization out of fears that the immunizations constituted a plot to reduce the country's Muslim population.
According to The Associated Press, the boycott was initiated after Pfizer faced accusations made by families and human rights groups of putting about 200 children at risk during what they claimed was a poorly managed meningitis study 11 years ago.