Depending on the perceived balance of risk and benefit, and on the perceived unnaturalness, some applications of gene technology appear more acceptable to the public than others. This study asks whether a person’s knowledge of biology affects their assessment of these factors differently. A random sample of the Danish population (n = 2000) was presented with questionnaires. The respondent’s knowledge was measured by a number of textbook questions on biology. The results indicated that knowledge increases the likelihood that a person will have differentiated opinions on medical and agricultural applications, but decreases the likelihood that he or she will differentiate between cisgenic and transgenic cereals. We discuss the implication that knowledge makes people more likely to base their acceptance on judgements of risks and benefits, rather than on judgements of naturalness. The article concludes that the effect of knowledge on acceptance cannot be generalised wholesale from one application, or method, to others.