Researchers have long been interested in understanding the “climate” in undergraduate engineering programs. These themes are particularly important for underrepresented groups in engineering such as women. We examine how students perceive climate and how these attitudes vary by gender. Using a repeated cross-sectional design, we compare populations at three institutions from 1995 (N=2279) to 2009 (N=1590) to understand how students' perceptions have changed. Overall, the climate seems to have improved from 1995 to 2009. However, women and men differ in some perceptions of climate. We analyzed student responses from a framework of considering structural factors, faculty factors, and factors related to student agency. Women and men respond similarly on items measuring quality of teaching, perceptions of being taken seriously by faculty, and perceptions of cooperative relationships between male and female students. However, women score differently from men on items measuring perceptions of fairness, participation in study groups, and issues of diversity. Improving recruitment and persistence of women requires a nuanced understanding of the climactic conditions that promote their success.