Women have about twice the risk of developing multiple sclerosis (MS) compared with men, a ratio that seems to be increasing. Most studies show that female patients seem to have a more favourable outcome of the disease. We studied the gender-specific impact of MS on health-related quality of life. We surveyed the population prevalence of MS patients in Ferrara, Italy. Data were extracted from the MS registry of the study area. Health-related quality of life was assessed using the MSQOL54 questionnaire. We analysed 370 patients (105 men and 265 women). They had worse scores than the general population in all health-related quality of life dimensions, ranging from 2.5 standard deviations (SD) lower for physical functioning to less than 0.5 standard deviations for mental health. Health-related quality of life scores were inversely correlated with disability scores. The impact of disability on health-related quality of life was higher for men than women regarding physical functioning (p < 0.01), vitality (p < 0.001), social functioning (p < 0.001), emotional wellbeing (p < 0.05) and mental health (p < 0.01). For scales reflecting mental health, a marked reduction with increasing disability was seen for men, while a linear reduction in the range of Expanded Disability Status Scale score 0-5 was reported for women, followed by no clear decrease for higher scores. We conclude that MS affects health-related quality of life in all of its dimensions. The impact of disability seems to be stronger among men, in particular for scales related to mental well-being. This could indicate that interventions should to be gender specific in order to better meet patients' needs.