For the first part of Ciepielowski's time at Buchenwald, he was set to hard labor. During this part of his imprisonment, he suffered a broken shoulder and serious injuries to his hand as a result of an amateur surgery, and as a result of his privations he wasted away to a weight of 46 kg.[1]
By late 1942, German forces were taking significant losses from typhus, particularly on the Russian front. Joachim Mrugowsky, head of the Waffen-SS's Hygiene Institute, had plans to produce a vaccine, but these plans were delayed by the bombing of his headquarters. Mrugowsky instead decided that the vaccine would be produced at Buchenwald, which was judged to be at lower risk of Allied bombing.[2] One of the camp's SS officers, the surgeon Erwin Ding-Schuler, needing researchers to staff his vaccine laboratory, pulled Ciepielowski to assist.[3] Ciepielowski would work in the camp hygiene department from July 1943 to April 1945.[1]
Compared to his conditions of confinement, Ciepielowski found himself in relative luxury. Prisoners in the hygiene unit had individual beds with clean linens, and were given additional rations of sugar, fat, and bread. They also ate the meat from the rabbits used in the laboratory.[4] Rabbits were used in the production of vaccine because the other methods were deemed less acceptable; one involved growing the vaccine in typhus-infected lice, which the SS did not wish to introduce into the camp, and another involved culturing the vaccine in chicken eggs, and chicken and eggs were both likely to be stolen for food.[2] Officially, two varieties of vaccine were produced in the camp - one meant for SS combat units, and another, of dubious quality, for the camp's inmates. Ciepielowski and his colleagues subverted this by producing a completely ineffective vaccine (made of water with small amounts of blood and formalin) to send to the front, while producing a high-quality, effective vaccine for other prisoners.[1] This was accomplished largely through the intervention of the biologist and physician Ludwik Fleck, who had been sent to Buchenwald from Auschwitz; Fleck almost immediately recognized the flaws in the prisoners' methods, but was convinced to assist them in secretly creating a real, potent vaccine, while manufacturing the fake vaccine for the SS.[2]
On one occasion, a Romanian researcher, suspicious after being unable to replicate the vaccine by the method utilized in the camp, submitted a paper demonstrating that the method was fraudulent. The paper made its way to Ding-Schuler, and put Ciepielowski and the other prison-researchers at risk of their lives. Ciepielowski successfully convinced Ding-Schuler that the Romanian doctor had erred, and authored a paper to that effect, to be published under Ding-Schuler's own name.[4] It would be one of a half-dozen papers Ciepielowski wrote (with fellow inmate Eugen Kogon as his medical clerk) to be published under the name of the SS officer.[5] Ciepielowski and the other researchers regarded Ding-Schuler (who had received his degree through party loyalty, rather than scholarship) to be a fool, easily manipulated due to his lack of medical knowledge.[2]