In 1998 a controversy occurred later named 'The Pusztai affair' wherein Protein scientist Árpád Pusztai went public with the initial results of unpublished research he was conducting at the Rowett Institute. He was investigating the possible effects of genetically modified potatoes upon rats and claimed that the GM potatoes stunted the growth and repressed the rats' immune systems while thickening their gut mucosa.

Initially Rowett Institute supported his comments but once he appeared on a British television programme and caused controversy across the UK, the Rowett Institute withdrew its support and his contract was not renewed by the research centre. Pusztai was thereby suspended and misconduct procedures were used to seize his data and ban him from speaking publicly.

Pusztai was criticized by the British Royal Society along with other scientists for making an announcement before his experiment was complete or peer-reviewed, even criticising the experiment's design, methodology and analysis. Some of his data from the experiments were published in 1999 in The Lancet, however, only five out of six peer reviewers approved of the study when it was published and this cause further controversy.