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While prior work has noted position biases in LLM-driven comparisons, these biases have not been systematically analyzed or linked to underlying preference structures. We present the first comprehensive study of position biases across multiple LLMs and two distinct domains: resume comparisons, representing a realistic high-stakes context, and color selection, which isolates position effects by removing confounding factors. We find strong and consistent order effects, including a quality-dependent shift: when all options are high quality, models favor the first option, but when quality is lower, they favor later options. We also identify a previously undocumented bias: a name bias, where certain names are favored despite controlling for demographic signals. To separate superficial tie-breaking from genuine distortions of judgment, we extend the rational choice framework to classify pairwise preferences as robust, fragile, or indifferent. Using this framework, we show that order effects can lead models to select strictly inferior options. These results indicate that LLMs exhibit distinct failure modes not documented in human decision-making. We also propose targeted mitigation strategies, including a novel use of the temperature parameter, to recover underlying preferences when order effects distort model behavior.<\/jats:p>","DOI":"10.1093\/pnasnexus\/pgag246","type":"journal-article","created":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T13:05:26Z","timestamp":1786453526000},"source":"Crossref","is-referenced-by-count":1,"title":["Fragile preferences: A deep dive into order effects in large language models"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4275-7476","authenticated-orcid":false,"given":"Haonan","family":"Yin","sequence":"first","affiliation":[{"name":"Department of Information Systems and Business Analytics, Ivy College of Business, Iowa State University , Ames, IA 50011 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4720-6826","authenticated-orcid":false,"given":"Shai","family":"Vardi","sequence":"additional","affiliation":[{"name":"Department of Information Systems, Muma College of Business, University of South Florida , Tampa, FL 33620 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8812-4232","authenticated-orcid":false,"given":"Vidyanand","family":"Choudhary","sequence":"additional","affiliation":[{"name":"Department of Information Systems, Paul Merage School of Business, University of California, Irvine , Irvine, CA 92697 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,11]]},"reference":[{"key":"2026081109011254300_pgag246-B1","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1111\/apt.18058","article-title":"Systematic review: the use of large language models as medical chatbots in digestive diseases","volume":"60","author":"Giuffr\u00e8","year":"2024","journal-title":"Aliment Pharmacol Ther"},{"key":"2026081109011254300_pgag246-B2","author":"Cook","year":"2025"},{"key":"2026081109011254300_pgag246-B3","first-page":"1578","volume-title":"Proceedings of the Seventh AAAI\/ACM Conference on AI, Ethics, and Society","author":"Wilson","year":"2024"},{"key":"2026081109011254300_pgag246-B4","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1017\/ilm.2024.46","article-title":"Regulation 2024\/1689 of the Eur. 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