Background The adoption of health information technology (HIT) is an important measure for improving healthcare quality and safety effected by many hospital factors, but it has not yet been estimated in the Mongolian healthcare field. This study examines how hospitals’ organisational characteristics influence the adoption of HIT in Mongolian tertiary and secondary care public hospitals. Methods А cross-sectional study involving the executive directors and quality managers at 39 hospitals. Data came from: (1) hospitals’ organisational characteristics (Mongolian Health Statistics, 2017), including hospital size, ownership type, health maintenance organisation (HMO) penetration, and hospital location; (2) questionnaires used to collect the adoption rate of HIT and HIT categories based on the Health Information and Management Systems Society’s classification (2002). The dependent variable was measured as numbers and the rate of HIT programs adopted included clinical, administrative and strategic information technologies (IT). A regression analysis was used to estimate the factors of impact on the adoption of clinical, administrative and strategic IT. Results On average, the number of HIT programs adopted reached 18, covering nine clinical IT programs, six administrative IT programs and three strategic IT programs. The adoption rate of overall HIT ranged between 29.02–38.05% with a mean of 33.29%. Regression analysis for organisational characteristics impact on HIT adoption found that the adoption of total HIT was positively associated with large hospital size (clinical IT: β=0.256, p< .001; administrative IT: β=0.3654, p< .001; strategic IT: β=0.0006, p<.001), ownership type (strategic IT: β=1995, p< .01), urban location (clinical IT: β=0.2840, p< .001, administrative IT: β=0.2256, p< .01; strategic IT: β=0.2256, p< .001), and HMO penetration (clinical IT: β=0.2560, p< .05, administrative IT: β=0.1985, p< .05; strategic IT: β=0.2236, p< .01). Conclusion Our study found that HIT adoption rate is poor, and HIT adoption is positively associated with hospitals’ organisational characteristics, such as large size, urban location, and HMO penetration. The profit ownership only positively contributes to strategic IT adoption. We concluded that hospitals with the above structural attributes conducive to more HIT adoption.