Background Patient groups represent the interest of their members when it comes to drug funding. Many patient groups receive grants from pharmaceutical companies that make products being considered for funding. This research examines whether there is an association between the positions that Canadian groups take about the products and conflicts of interest with the companies. Methods The Common Drug Review (CDR) and panCanadian Oncology Drug Review (pCODR) make recommendations to Canadian provincial and federal drug plans about funding particular drug-indications. Both utilize input from patient groups in making their recommendations. Patient group submissions are available from both organizations and these submissions contain statements about conflicts of interest. Views of the patient groups, with and without a conflict with the company making the drug under consideration and without any conflicts at all, were assessed and then compared with the recommendations from CDR and pCODR. Results There was a total of 222 reports for drug-indications. There were 372 submissions from 93 different patient groups. Groups declared a total of 1896 conflicts with drug companies in 324 (87.1%) individual submissions. There were 268 submissions where groups declared a conflict with the company making the product or said they had no conflict. Irrespective of whether there was a conflict, the views of patient groups about the drug-indications under consideration were the same. There was no statistically significant difference between views of patient groups and the recommendations from CDR and/or pCODR. Conclusions The large majority of patient groups making submissions about funding of particular drug-indications had conflicts with the companies making the products and their views about the products were almost always positive. This association between funding and views needs to be further investigated to determine if a true cause and effect exists.