Background Many patient organisations collaborate with drug companies, resulting in concerns about commercial agendas influencing patient advocacy. We contribute to an international body of knowledge on patient organisation-industry relations by considering payments reported in the industry’s centralised ‘collaboration database’ in Sweden. We also investigate possible commercial motives behind the funding by assessing its association with drug commercialisation. Methods Our primary data source were 1,337 payment reports from 2014–2018. After extraction and coding, we analysed the data descriptively, calculating the number, value and distribution of payments for various units of analysis, e.g. individual companies, diseases and payment goals. The association between drug commercialisation and patient organisation funding was assessed by, first, the concordance between leading companies marketing drugs in specific diseases and their funding of corresponding patient organisations and, second, the correlation between new drugs in broader condition areas and payments to corresponding patient organisations. Results 46 companies reported paying €6,449.224 (median €2,411; IQR €1,024–4,569) to 77 patient organisations, but ten companies provided 67% of the funding. Small payments dominated, many of which covered costs of events organised by patient organisations. An association existed between drug commercialisation and industry funding. Companies supported patient organisations in diseases linked to their drug portfolios, with the top 3 condition areas in terms of funding–cancer; endocrine, nutritional and metabolic disorders; and infectious and parasitic disorders–accounting for 63% of new drugs and 56% of the funding. Conclusion This study reveals close and widespread ties between patient organisations and drug companies. A relatively few number of companies dominated the funding landscape by supporting patient organisations in disease areas linked to their drug portfolios. This commercially motivated funding may contribute to inequalities in resource and influence between patient organisations. The association between drug commercialisation and industry funding is also worrying because of the therapeutic uncertainty of many new drugs. Our analysis benefited from the existence of a centralised database of payments–which should be adopted by other countries too–but databases should be downloadable in an analysable format to permit efficient and independent analysis.