Background The aging population and increasing chronic diseases make a tremendous burden on the health care system. The study evaluated the relationship between comorbidity indices and common geriatric syndromes. Methods A total of 366 patients who were hospitalized in a university geriatric inpatient service were included in the study. Sociodemographic characteristics, laboratory findings, and comprehensive geriatric assessment(CGA) parameters were recorded. Malnutrition, urinary incontinence, frailty, polypharmacy, falls, orthostatic hypotension, depression, and cognitive performance were evaluated. Comorbidities were ranked using the Charlson Comorbidity Index(CCI), Elixhauser Comorbidity Index(ECM), Geriatric Index of Comorbidity(GIC), and Medicine Comorbidity Index(MCI). Because, the CCI is a valid and reliable tool used in different clinical settings and diseases, patients with CCI score higher than four was accepted as multimorbid. Additionally, the relationship between geriatric syndromes and comorbidity indices was assessed with regression analysis. Results Patients’ mean age was 76.2 ± 7.25 years(67.8% female). The age and sex of multimorbid patients according to the CCI were not different compared to others. The multimorbid group had a higher rate of dementia and polypharmacy among geriatric syndromes. All four indices were associated with frailty and polypharmacy(p < 0.05). CCI and ECM scores were related to dementia, polypharmacy, and frailty. Moreover, CCI was also associated with separately slow walking speed and low muscle strength. On the other hand, unlike CCI, ECM was associated with malnutrition. Conclusions In the study comparing the four comorbidity indices, it is revealed that none of the indices is sufficient to use alone in geriatric practice. New indices should be developed considering the complexity of the geriatric cases and the limitations of the existing indices.