Women with long-standing coeliac disease express poorer health-related quality of life (HRQoL) than men do for unclear reasons. This led us to explore differences in their understanding of HRQoL using a phenomenographic approach. We interviewed 10 coeliac subjects (mean age 57 years, range 35–73) who had been on a gluten-free diet for 10 years and had scored either high or low in the Short Form 36 Health Survey (SF-36) General Health and Vitality scales. Three dimensions were revealed that pertained to their perception of HRQoL: bodily sensations, social consequences and coping strategies. Within these, the women experienced more bowel symptoms than men did, despite keeping to a strict diet. This item was the only one predicting the SF-36 scores. The women also described more distress caused by the restrictions in daily life, closely related to their controlling of food contents. The coeliac men took advantage of using a problem-oriented coping approach while the women seeking an emotionally oriented strategy showed less satisfaction with the outcome. We conclude that the intriguing difference in HRQoL between coeliac men and women may have some of its origin in the way living with the disorder is conceptualized and coped with. The results imply that in the management of coeliac patients, gender-related aspects need to be taken into account to improve treatment outcome.