The emergence of electronic health records (EHR) offers unprecedented opportunities to streamline data collection for biomedical research. Nevertheless, limited information exists describing participant’s perspectives of leveraging EHR for research purposes in vulnerable populations. The purpose of our study was to explore perspectives of breastfeeding and pregnant women on using EHRs for research, focusing on the specific factors that would prevent research participation. Twenty-nine pregnant and breastfeeding mothers from Alachua County were recruited to complete in-depth semi-structured interviews. Transcripts were organized and coded using NVivo and coded data was thematically analyzed using constant comparison. Three major themes emerged when mothers were asked about releasing their EHR for research purposes: privacy and confidentiality, trust, and child autonomy. Our results also revealed that concerns for using EHR for research purposes were devoted to the release of infant’s EHRs as well as stigmatizing conditions such as mental health and sexual history. Release of electronic health records for research purposes was conditional on factors related to participant privacy and confidentiality among pregnant and breastfeeding women. Collectively, our results demonstrate participant’s perspectives related to privacy and confidentiality are critical factors that should be considered when using EHRs for research purposes, particularly with regards to vulnerable populations.