AIMS: Research has raised concerns about gender bias in medicine, i.e. that men and women might be treated differently due to gender-stereotyped attitudes among physicians. The authors investigated gender differences in medical management of a common health problem, irritable bowel syndrome (IBS). METHOD: In a national examination for Swedish house officers, the examinees were allocated to suggest management of IBS in either a male or female paper-patient. The case description was identical in both genders with the exception of prior prostate and gynaecological symptoms. The open answers were coded for analysis. A total of 289 physicians (45% women) participated. Chi-squared tests were used to measure differences in proportions. RESULTS: In variables focusing on medication, weight, gynaecological problems, tobacco, alcohol, thyroid function, proposed diagnoses, X-ray of the colon, and advice about lifestyle, significant or close to significant gender differences were seen. Both male and female physicians made gender differences but they did not show the same pattern of differences. CONCLUSIONS: The results suggest that gender bias is involved in medical management of IBS but men and women physicians may show disparate patterns of gender bias. There is a need for larger studies on gender differences in medical management with designs making it possible to consider the gender of both the patient and the physician. Furthermore, the results call attention to 'knowledge-mediated gender bias', a phenomenon implying that once knowledge about gender differences in a condition has been established, this might in fact cause gender-biased assessments of individual patients in clinical practice.