The aim of the paper is to clarify the concept of scientific ignorance: what is it, what are its sources, and when is it epistemically detrimental to science. While some sources of scientific ignorance come inevitably with the process of knowledge acquisition, others are deliberately created. The former includes selection process,s, inductive reasoning, and cognitive biases, while the latter includes scientific fraud. Another important source of scientific ignorance appears when scientists introduce methodological biases through micro-decisions in the research process. I provide three examples from medical research to illustrate this point. I argue further that methodological biases present a challenge, in so far as they are no easily classifiable as deliberate: they might also be the result of entrenched research practices within a scientific community. Strategies to identify and prevent methodological biases in research should take into account such difference.