Background: Studies have shown that the use of medicines with anti-cholinergic (Ach) properties can increase elderly patients’ risk of experiencing falls, confusion, and longer hospital stays (LOS). These adverse effects are preventable with appropriate intervention. Little is known about the use of medicines with Ach properties and their impact on Malaysian elderly patients. This study aimed to investigate the use of medicines with Ach properties and their impact on fall risk, confusion, and longer LOS among hospitalised elderly patients. Methods: This study utilised a cross-sectional design and was conducted at a single centre where convenience sampling was employed to collect data from elderly patients (> 60 years) admitted to geriatric and medical wards at Hospital Tuanku Ja’afar during a 2-month period (July 2017–August 2017). Patients were excluded from this study if their hospital admission was planned for an elective procedure or if neurocognitive and hepatic impairment were diagnosed prior to the hospital admission. Medicines with Ach properties were identified and classified according to the anti-cholinergic drug scale (ADS). Univariate and multiple logistic regression statistical analyses were performed to assess its impacts on falls, confusion, and LOS. Results: A total of 145 elderly patients with a mean age of 71.59 years old (SD = 8.02) were included in the study. Fifty-two percent of the participants were female, and the average hospital stay was 6 days (SD = 2.09). Medicines with Ach properties were administered in 62% (n = 90) of the cases. The most commonly prescribed medicine with Ach properties was furosemide (n = 59), followed by ranitidine (n = 44), warfarin (n = 23), and methylprednisolone (n = 22). Compared to patients who did not receive medicines with Ach properties, patients who received them had a significantly higher risk of falls [odds ratios (OR) = 2.61; 95%CI: 1.18, 5.78; P = 0.018], confusion (OR = 3.60; 95%CI: 1.55, 8.36; P = 0.003), and LOS (OR = 4.83; 95%CI: 2.13, 10.94; P < 0.001). Multiple comorbidities also showed a significantly increased risk of falls (OR = 3.03; 95%CI: 1.29, 7.07; P = 0.010). Conclusion: Medicines with Ach properties had a significant impact on elderly patients’ health. Strategies for rationally prescribing medicines with Ach properties to Malaysian elderly patients need to be improved and be recognised as an important public health priority.