Objectives To compare potentially inappropriate prescribing (PIP) according to the clinical judgement of the pharmacist with PIP according to explicit STOPP-START criteria in institutionalised and hospitalised patients with multiple pathologies. To describe and compare the main pharmacological groups involved and determine the factors associated with the detection of PIP in these patients. Method A prospective multicentre observational study of institutionalised and hospitalised multipathology patients aged >65 years. A specialised pharmacist used his best clinical judgement to detect PIP based on a comprehensive review of the complete chronic treatment of patients, which is an essential activity in interdisciplinary care. STOPP-START criteria were used as an aid tool to detect PIP. The main variable was the number of PIP incidents detected. Results Detected PIP incidents were analysed in 338 patients. Clinical judgement detected more PIP incidents (35%) than did STOPP-START criteria. More PIP incidents unrelated to these criteria were detected in institutionalised patients than in hospitalised patients. Clinical judgement mainly detected PIP incidents related to incorrect doses and drug interactions (p<0.001); however, STOPP-START criteria mainly detected PIP incidents related to drug duplication and insufficiently treated diagnosis or symptoms (p=0.001 and p<0.001). In total, 93.8% of the PIP incidents were detected in polypharmacy patients (>= 5 drugs). Institutionalised and high-level polypharmacy (>= 10 drugs) patients were at the highest risk of PIP. Conclusions A large number of PIP incidents were detected in institutionalised and hospitalised patients with multiple pathologies. The inclusion of a pharmacist in the multidisciplinary team facilitated the detection of PIP incidents, particularly in the institutionalised population and patients treated with high-level polypharmacy which were not detected by explicit STOPP-START criteria.