Converging evidence from genetics suggests that disruptions in the development of healthy neural circuits underlie and precede behavioral signs of autism spectrum disorder (ASD). Imaging and electrophysiological studies have quantified aberrant neural connectivity in children and adults with ASD, with a wide range of (and difficult to generalize) results owing to the heterogeneity of methods and populations studied. Examination of functional connectivity patterns in infants at risk for ASD, well before behavioral signs and confounding comorbidities emerge, can elucidate early brain changes that relate more directly to putative biological mechanisms. These findings can, in turn, inform more targeted studies of biomarkers of functional connectivity in childhood. Here, we present innovative approaches to the investigation of neural connectivity in infants at risk for ASD, through electroencephalography (EEG: Tran, Haartsen) and magnetic resonance imaging (MRI: Ciarrusta, Chen). In the context of these data that demonstrate atypical connectivity patterns both at rest and during social information processing in early infancy, we will discuss (Jones) methodological challenges and opportunities in infant connectivity studies, consider the generalizability of these findings, and share experiences from infant imaging consortia on the value of and next steps in large-scale studies of infant brain development in ASD.