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How does masculinity intersect with for-profit motives in commercial science? Research has shown that, while there is growing gender parity in STEM fields, women commercialize their research less than men. This disparity is often observed by analyzing research outcomes, specifically patents, but less is known about the processes that create these conditions. Identifying these processes requires on-the-ground qualitative analysis. Building on five years of ethnographic fieldwork, 60 qualitative interviews, and content analysis, this paper analyzes the intersection of commercial science and masculinity in relation to both relational and discursive social structures. For relational social structures, I find that the prominence of masculine teams and organizations, as well as the dynamics of competition, benefit men while simultaneously constraining women’s success in commercial contexts. For discursive social structures, I find that discourse around ‘innovation’ directs resources to men, allowing them to support more students, and thus train new commercial scientists, while discourse around ‘users’ of technology also reproduce gender inequality. When there are primarily men in the room inventing to technology, women’s voices and experiences often go unheard. I conclude that gendered organization of commercial science channels resources to men and creates opportunities for young men to gain experience valued by the market. Conversely, these organization patterns constrain women’s access to resources, and creates new axes for women to experience hostility in the workplace.