BACKGROUND: Individuals with vitamin B12 deficiency (including pernicious anaemia) often report being 'let down' or stigmatised by general practice systems and policy, and choose instead to self-medicate via injection; the association between this and perceptions of safe primary care in this group of people is unknown. AIM: To examine the association between self-medication for vitamin B12 deficiency and patient-reported safety in primary care. DESIGN AND SETTING: A UK cross-sectional online survey. METHOD: The survey consisted of the three components: demographics; the validated Primary Care Patient Measure of Safety; and questions about self-medication for vitamin B12 deficiency. Multivariable logistic regression analyses and thematic synthesis were undertaken. RESULTS: Responses from 1297 participants indicated 508 (39.2%) self-medicated via injection. Perceived primary care safety was low. Those who self-medicated via injection reported a significantly lower level of patient safety in primary care including adverse patient-related factors (odds ratio 0.82, 95% confidence interval = 0.73 to 0.92), and patients >34 years of age were significantly more likely to self-medicate via injection. Many reported that treatment under the guidance of a clinician was preferable to self-medication, but felt they had no other choice to regain quality of life. Almost half felt that the doctor did not always consider what they wanted for their care. CONCLUSION: To the authors' knowledge, this is the largest study to date examining patient safety and vitamin B12 deficiency. It found that four out of 10 patients with B12 deficiency self-medicate via injection. Patients who self-medicated perceived primary care as less safe. Providing patient-centred care and treating these patients with dignity and respect is a policy priority to reduce unsafe health behaviours.