Rationale: Childhood vaccination is a safe and effective way of reducing infectious diseases. Yet, public confidence in vaccination is waning, driven in part by the ‘manufacture of doubt’ by anti-vaccination activists and websites. However, there is little research examining the psychological underpinnings of anti-vaccination rhetoric among parents. Objectives: Here, we examined the structure and moral roots of anti-vaccination attitudes amongst Australian parents active on social media parenting sites. Methods: Participants (N = 296) completed questionnaires assessing their vaccination attitudes, behavioural intentions, and moral preferences. Results: Using Latent Profile Analysis, we identified three profiles (i.e., groups), interpretable as vaccine “accepters”, “fence sitters”, and “rejecters”, each characterised by a distinct pattern of vaccination attitudes and moral preferences. Accepters exhibited positive vaccination attitudes and strong intentions to vaccinate; rejecters exhibited the opposite pattern of responses; whilst fence sitters exhibited an intermediate pattern of responses. Compared to accepters, rejecters and fence sitters exhibited a heightened moral preference for liberty (belief in the rights of the individual) and harm (concern about the wellbeing of others). Compared to acceptors and fence sitters, rejecters exhibited a heightened moral preference for purity (an abhorrence for impurity of body), and a diminished moral preference for authority (deference to those in positions of power). Conclusion: Given the sensitivity of fence sitters and rejecters to liberty-related moral concerns, our research cautions against the use of adversarial approaches—e.g., No Jab, No Pay legislation—that promote vaccination uptake by restricting parental freedoms, as they may backfire amongst parents ambivalent toward vaccination.