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Medications with anticholinergic properties, although widely used, may negatively affect cognitive and functional status in older patients. To date there is still no standardized method to quantify anticholinergic exposure. We analyzed the relationship of two different tools for the evaluation of the anticholinergic drug burden with cognitive and functional impairment in a sample of older hospitalized patients. A retrospective and longitudinal analysis with 1-year follow-up of 1123 older hospitalized patients enrolled in seven Italian acute care wards was conducted. We assessed anticholinergic burden with the Anticholinergic Cognitive Burden (ACB) and Anticholinergic Risk Scale (ARS). Cognitive and functional status were evaluated at hospital discharge and during follow-up (3, 6, 12 months) using the Mini Mental State Examination (MMSE) and five basic activities of daily living (ADLs). Associations between anticholinergic burden and cognitive decline and incident disability were estimated using linear regression models for repeated measures and logistic models, respectively. The mean age of the study population was 81 ± 7.5 years. ACB and ARS classifications showed low correlation (Spearman’s rho = 0.39–0.43). Anticholinergic burden increased during hospitalization and was associated with cognitive and functional status. Patients with an ARS of ≥ 1 at discharge had significantly lower baseline MMSE scores (ARS = 0: 23.1; ARS ≥ 1: 20.8; p = 0.002) and during follow-up presented a significantly steeper MMSE score decline (− 0.15/month). Moreover, patients with an ACB of ≥ 1 at discharge had an almost threefold increased risk of developing disability (odds ratio 2.77, 95% confidence interval 1.39–5.54). ACB and ARS have only a moderate degree of correlation. Use of drugs with anticholinergic properties in elderly patients is independently associated with cognitive and functional decline.