In recent decades an important social movement related to Complementary and AlternativeMedicine has been identified worldwide. In Brazil, although homeopathy was recognized as a specialist medical area in 1980, few medical schools offer courses related to it. In a previous study, 176 resident doctors at the University of Campinas Medical School were interviewed and 86 (49%) rejected homeopathy as a subject in the core medical curriculum. Thus, this qualitative study was conducted to understand their reasons for refusing. 20 residents from 15 different specialist areas were interviewed. Very few of them admitted to a lack of knowledge for making a judgment abouthomeopathy; none of them made a conscientious objection to it; and the majority demonstrated prejudice, affirming that there is not enough scientific evidence to support homeopathy, defending their position based on personal opinion, limited clinical practice and on information circulated in the mass media. Finally, resident doctors’ prejudices against homeopathy can be extended to practices other than allopathic medicine.