Marginalia has been studied as discourse, as historical documentation, and as evidence of reader response. As many academic texts are now available electronically, it seems a natural step to incorporate the interactive, social functions of the Web 2.0. Digital marginalia in an academic publishing context has been a largely unsuccessful venture to this date, yet there are several promising developments. Tools have emerged that enable readers annotate online texts in an approximation of paper-based marginalia, with the additional affordances of two- (or many-) way discourse, digital archiving, and the ability to hide the annotations. This paper reviews the contemporary practices of digital marginalia, narrowing in to focus on digital marginalia as a form of academic discourse and peer review. I analyze several case studies of digital marginalia and discourse within this context, including Nature’s trial of open peer review, PLoS One and PubPeer’s systems, as well as my own experience using open peer review with Hypothes.is in a special “disrupted” issue of the Journal of Media Practice. The paper examines the relative success of these initiatives, attitudes toward open peer review, and concludes with some promising developments for the future of digital marginalia and discourse in academic publishing.