Background Despite having a large indigenous population, little is known about the differences in COVID-19-related health outcomes between indigenous and non-indigenous patients in Mexico. The aim of this study is to analyse the variation in hospitalisation and death between indigenous and non-indigenous patients with COVID-19 to guide future policies and clinical practice.

Methods We used data from the Mexican Ministry of Health (MoH) to study the hospitalisation and death of adults with laboratory-confirmed SARS-CoV-2 in MoH facilities between 1 March 2020 and 28 February 2021. Predicted probabilities of hospitalisation and death were adjusted for sociodemographic and presentation to care characteristics as well as municipal social deprivation index and health jurisdiction-level index of human resource and hospital equipment availability.

Results Of 465 676 hospitalised adults with COVID-19, 5873 (1.3%) were identified as indigenous. Indigenous patients had higher odds of hospitalisation (adjusted OR (aOR)=1.9, 95% CI 1.8 to 2.0), death (aOR=1.3, 95% CI 1.1 to 1. 3) and early mortality (aOR=1.2, 95% CI 1.0 to 1.4), compared with non-indigenous patients. Living in municipalities with high social deprivation was associated with a higher risk of hospitalisation and early death. Living in areas with low healthcare resources was associated with a higher risk of hospitalisation but not death. Being male, aged 51 years or older, having diabetes, hypertension and obesity were associated with an incremental probability of hospitalisation and death among indigenous patients.

Conclusions Indigenous patients with COVID-19 in Mexico have a higher risk of hospitalisation and death than non-indigenous individuals. Our findings can guide future efforts to protect this population from SARS-CoV-2 infection and associated outcomes.