Biology‐based engineering disciplines have been the most successful at recruiting women into engineering. An analysis of gender differences in student experiences in such disciplines helps illuminate ways to combat the under‐representation of women in engineering. This article examines the academic backgrounds, expressed interests, and student experiences of 424 women and men in biology‐based engineering programs throughout the country. Gender similarities in the broad engineering activities of design, building, and analysis were found. Gender differences were identified in the applications of these activities. Male students were significantly more interested in the applications in the areas of agriculture, automation, and irrigation, while female students were significantly more interested in the areas of biochemical engineering, biomedicine, and social responsibility. These results suggest that recruiting and retention of women in biology‐based engineering disciplines can be promoted by selecting appropriate application areas without sacrificing emphasis on overall engineering skills.