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Background Drug related problems (DRPs) are frequent and cause suffering for patients and substantial costs for society. Multi-dose drug dispensing (MDDD) is a service by which patients receive their medication packed in bags with one unit for each dose occasion. The clinical decision support system (CDSS) electronic expert support (EES) analyses patients' prescriptions in the Swedish national e-prescription repository and provides alerts if potential DRPs are detected, i.e. drug-drug interactions, duplicate therapy, drug-disease contraindications, high dose, gender warnings, geriatric, and paediatric alerts. Objective To analyse potential DRPs in patients with MDDD, detected by means of EES. Setting A register study of all electronically stored prescriptions for patients with MDDD in Sweden (n = 180,059) March 5-June 5, 2013. Method Drug use and potential DRPs detected in the study population during the 3 month study period by EES were analysed. The potential DRPs were analysed in relation to patients' age, gender, number of drugs, and type of medication. Main outcome measure Prevalence of potential DRPs measured as EES alerts. Results The study population was on average 75.8 years of age (± 17.5, range 1-110) and had 10.0 different medications (± 4.7, range 1-53). EES alerted for potential DRPs in 76 % of the population with a mean of 2.2 alerts per patient (± 2.4, range 0-27). The older patients received a lower number of alerts compared to younger patients despite having a higher number of drugs. The most frequent alert categories were drug-drug interactions (37 % of all alerts), duplicate therapy (30 %), and geriatric warnings for high dose or inappropriate drugs (23 %). Psycholeptics, psychoanaleptics, antithrombotic agents, anti-epileptics, renin-angiotensin system agents, and analgesics represented 71 % of all drugs involved in alerts. Conclusions EES detected potential DRPs in the majority of patients with MDDD. The number of potential DRPs was associated with the number of drugs, age, gender, and type of medication. A CDSS such as EES might be a useful tool for physicians and pharmacists to assist in the important task of monitoring patients with MDDD for potential DRPs.