The aim of the present study was to investigate gender differences in students’ health habits and motivation for a healthy lifestyle. The sample of students comprised a probability systematic stratified sample from each department at a small university in the south-west of Sweden (n = 479). A questionnaire created for this study was used for data collection. Self-rated health was measured by number of health complaints, where good health was defined as having less than three health complaints during the last month. A healthy lifestyle index was computed on habits related to smoking, alcohol consumption, food habits, physical activity and stress. Female students had healthier habits related to alcohol consumption and nutrition but were more stressed. Male students showed a high level of overweight and obesity and were less interested in nutrition advice and health enhancing activities. The gender differences are discussed in relation to the impact of stress on female students’ health, and the risk for male students in having unhealthy nutritional habits in combination with being physically inactive and drinking too much alcohol.