Identifying factors associated with disruptions in early neurodevelopment is imperative for promoting the health and wellbeing of children. We describe a design framework for biospecimen collection for the forthcoming HEALthy Brain and Child Development (HBCD) study, which seeks to establish a large cohort of pregnant women throughout the USA and follow their children into middle childhood. Biospecimens and biological outcomes of interest, together with validated questionnaires and other measures, may help to disentangle the effect of prenatal exposures from social and environment factors that extend across the prenatal and postnatal periods, including early life adversity (ELA). Biospecimen selection is discussed across four domains of interest: (a) substance use exposure, (b) other environmental exposures, (c) genomics and epigenomics, and (d) other biological markers of neurodevelopment and putative moderators and mediators of developmental effects. HBCD biospecimen working group recommendations were based on nine guiding principles including utility as a biomarker to assess neurodevelopment; feasibility of collection during critical periods of exposure with a broad detection window; logistics and cost of specimen collection, storage, and transportation; cultural acceptability; minimal invasiveness; flexibility; high sensitivity and specificity; anticipated expertise and infrastructure at participating sites; and availability of informative alternative non-biological measures. The proposed essential and recommended biospecimens will need to be integrated with the recommendations from other HBCD working groups to ascertain overall burden for the research participants and families, feasibility of multi-modal collection at each study visit, cost, and implications for recruitment and retention, as well as any potential legal repercussions.