Gender disparities in science, technology, engineering, and mathematics (STEM) are well documented, yet little is known about how women and men students establish social relationships with research mentors and peers and how that shapes their experiences in STEM. We conducted a series of interviews with 17 undergraduate students from a Hispanic majority institution regarding their participation in STEM-focused summer research programs at nine universities. Differences in levels of comfort in relationships were present when comparing men and women. Women students expressed comfort in relationships with mentors who provided psychosocial mentoring, were available to answer questions, and were of the same gender; they expressed some social discomfort in informal interactions with mentors. Men students felt comfortable with mentors who provided limited guidance, little psychosocial mentoring, and opportunities for informal interactions. In terms of peer relationships, women sought out the confidence of a few similar peers, while men were comfortable with a wide variety of peers. Men's greater comfort with social relationships seemed to reflect their affinity with the masculine-dominated culture of STEM. For women, cultivating safe spaces through relationships with supportive peers and working with same-gender faculty mentors seemed to mitigate some of the discomforting aspects of their STEM research experiences.