Respect for autonomy is problematic in relation to public health programmes such as vaccination, as the success of such programmes depends on widespread compliance. European countries have different policies for dealing with objectors to vaccination programmes. In some countries compliance is compulsory, while in others objectors are exempted or allowed to enter the programme under specific conditions. In this paper I argue that the objectors should not be treated as a homogenous group as is done in the above-mentioned policies. Objectors have different arguments for not participating in vaccination programmes. Considering the value of respect for autonomy, some but not all of these arguments need to be accommodated by authorities. The concept of 'narrative autonomy' provides criteria to distinguish between tenable and untenable claims to the right to refuse vaccination. Narrative autonomy understands autonomy as essentially linked to identity, as this provides the moral framework with which we assess our first-order preferences. The above-mentioned concept of autonomy is derived from the concept of narrative identity as described by Marya Schechtman. She suggests that the application of the Articulation Constraint and the Reality Constraint enables us to establish the validity of personal narratives. Additionally, form and content features of identity, as proposed by Anthony Laden, will be used as criteria to establish the compatibility of the defectors' arguments with shared scientific and political values. Such compatibility is essential to accommodate respect for autonomy in the context of public health.