Risk assessments by expert witnesses appointed by the Family Court of Australia (FCA), and as informed by findings of any investigations by police and child protection agencies, play a critical role in the adjudication of custody disputes involving allegations of child sex abuse. This study focuses on the contribution made by these independent advisors as documented in the FCA trial transcripts of a sample of 62 such cases in the period 2012–2016. Analysis reveals that those responsible for assessing risk shared a concern for an emerging pattern of applicant responsibility for systems abuse, in conjunction with emotional abuse, as a significant child protection issue. It also raises issues for the Court when there are multiple risk assessments coming from experts who bring different disciplinary and organisational perspectives. As an exploratory study, the implications of these findings need to be viewed through the lens of protecting the best interests of the child.