Abstract Background In Germany, complementary and alternative medicine (CAM) in primary health care is offered by general practitioners (GPs) and by natural health practitioners, so called ‘Heilpraktiker’ (HPs). Considering the steadily growing number of unregulated HPs, the aim of the study was to assess characteristics of patients consulting HPs in comparison to patients consulting GPs. Methods In a cross-sectional study, patients of randomly selected GPs and HPs were asked to complete a questionnaire about their health care status, health care behavior, and symptoms rated on the Measure Yourself Medical Outcome Profile (MYMOP-D). Patient groups were compared based on health care provider (HP, GP with high use of CAM (CAM-GP), and GP with no/little use of CAM (nCAM-GP)) using Kruskal-Wallis tests and analyses of variance (ANOVA). Results Altogether, 567 patients (91 of 11 HPs, 223 of 15 CAM-GPs, 253 of 19 nCAM-GPs) filled in the questionnaire. Patients of HPs had a higher education level and were more often female. The most common reason for encounter among all three groups were musculoskeletal problems (30.2–31.1 %). Patients seeing HPs reported more psychological (4.4 % vs. 17.8 %), but less respiratory problems (19.9 % vs. 7.8 %), and longer symptom duration (>5 years: 21.1 % vs. 40.7 %), than patients of nCAM-GPs. Conclusions The high percentage of patients with psychological illness and chronic health problems consulting HPs demonstrates the urgent need for action with regard to CAM therapy in primary care and regulation of natural health practitioners. Appropriate measures with regard to quality and patient safety should be taken given the growing numbers of HPs and the absence of a regulatory body.