Introduction: Since April 2022, indexing in Medline has been done through automatic indexing using an algorithm. According to PubMed, quality assurance processes are in place to ensure the accuracy of the decisions, including citations with recognized ambiguities. Humans may still participate in the indexing process by reviewing and curating the results.

Objective: Despite the introduction of the MeSH term Intersex Persons in 2020, as of January 2025, only 13 articles are tagged with the term. None of these articles were indexed using automatic indexing. This paper examines the systemic exclusion of intersex-related literature within the indexing framework in Medline.

Methods: In July 2024, a search was conducted to identify citations that included intersex in the title and abstract. The search was limited to articles published from 2020 onwards and excluded the 13 articles with the Intersex Person MeSH term.

Results: A total of 500 articles were identified. After excluding animal studies and studies that were not yet indexed, 228 articles remained. A definitive decision about the indexing could not be made for 24 articles. Of the 228 articles, 167 (73.2%) were indexed using automatic indexing and the remaining 61 (26.8%) involved humans. After analyzing the full-text, it was determined that 59.9% of the automatic indexed articles and 45.9% of the manually indexed articles should have been tagged with the Intersex Persons MeSH term.

Conclusion: This study reveals significant gaps in the Medline indexing process concerning intersex-related literature. These findings indicate systemic issues in both automatic and manual indexing processes, suggesting that intersex-related research is often misunderstood, misclassified and invisible.