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Background Patients suffering from cancer often make use of complementary and alternative medicine (CAM). Only few data exist on the prevalence and clinical significance of interactions of a biological CAM method and conventional drugs. Methods From February 2014 to March 2016, consecutive patients from five oncological practices in Germany were asked to fulfill a standardized questionnaire regarding use of CAM. Data on diagnosis, date of first diagnosis, ECOG and the past and current treatment were derived from the patients’ files. Interactions were evaluated by systematically using a database on potential interactions. Results From 1000 patients asked to participate, we received a total of 720 questionnaires of which 711 were completed and eligible for evaluation. 29% of the patients reported any CAM usage. Women showed a significantly higher use of CAM with 35.6 versus 23.6% of men. For 54.9% of CAM users (15.9% of all patients), we found a combination of conventional drugs and biological based CAM methods with a risk for interactions. Vitamins A, C and E were the most frequently used CAM substances in these cases (39.3%), followed by herbs with 17.5%. Conclusion There was a risk of interactions between a biological CAM method and conventional drugs in 54.9% of the patients using CAM. To raise knowledge on interactions a better training for doctors with respect to CAM is strongly needed. Furthermore, patients’ awareness should also be raised and communication between physician and patient on the topic improved.