Background Parenting issues can affect physicians' choice of specialty or subspecialty, as well as their selection of individual training programs, because of the distinctive challenges facing residents and fellows with children. Specific information about how residents perceive these challenges is limited. Objective We sought to better understand the challenges associated with parenting during residency and fellowship training in order to inform policy and research. Methods In 2017, a voluntary online questionnaire was distributed to all 2214 Partners HealthCare graduate medical education trainees across 285 training programs. The survey queried attitudes of and about trainees with children and assessed needs and experiences related to parental leave, lactation, and childcare. Responses were compared between subgroups, including gender, surgical versus nonsurgical specialty, parental status, and whether the respondent was planning to become a parent. Results A total of 578 trainees (26%) responded to the questionnaire. Of these, 195 (34%) became parents during training. An additional 298 (52%) planned to become parents during training. Respondents overwhelmingly agreed that their institution should support trainees with children (95%) and that doing so is important for trainee wellness (98%). However, 25% felt that trainees with children burden trainees without children. Childcare access, affordability, and availability for sufficient hours were identified as key challenges, along with issues related to parental leave, lactation facilities, and effect on peers. Conclusions This survey highlights trainees' perspectives about parenting during their clinical training, signaling parental leave, lactation facilities, and childcare access and affordability as particular challenges and potential targets for future interventions.