Objective Our objective was to assess the occurrence and determinants of selective citation in scientific publications on Strachan's original hygiene hypothesis. His hypothesis states that lack of exposure to infections in early childhood increases the risk of rhinitis. Setting Web of Science Core Collection. Participants We identified 110 publications in this network, consisting of 5551 potential citations. Primary and secondary outcome measures Whether a citation occurs or not, measured and analysed according to the preregistered protocol. Results We found evidence for citation bias in this field: publications supportive of the hypothesis were cited more often than non-supportive publications (OR adjusted for study design [adjOR] 2.2, 95% CI 1.6 to 3.1), and the same was the case for publications with mixed findings (adjOR 3.1, 95% CI 2.2 to 4.5). Other relevant determinants for citation were type of exposure, specificity, journal impact factor, authority and self-citation. Surprisingly, prospective cohort studies were cited less often than other empirical studies. Conclusions There is clear evidence for selective citation in this research field, and particularly for citation bias.