Abstract Background In Germany, homeless people are entitled to health care within the regular health care system. However, due to their specific living conditions they make little use of these services. In 2013, three Medical centres for the homeless (MCH) were opened in Hamburg to provide general health care. This study aims to analyse the consultation reasons and diagnoses prevalent among the homeless in comparison to regular primary care patients. It also examines the means and obstacles of integrating the homeless into Germany’s regular health care system. Methods From 2013 to 2014, routine medical data of all patients of the MCH consenting to participate in the study were analysed descriptively, in particular consultation reasons (categorised by ICPC-2), ICD-10 diagnoses and data on health insurance status and the use of the regular health care system. Consultation reasons and diagnoses of homeless patients were compared descriptively with data from regular general practices. Additionally, anonymous data on patient numbers, gender and insurance status was exported from the MCH’s software and analysed descriptively for the years 2013 to 2020. Results A total of 840 homeless patients in 2013 and 2014 gave consent to the evaluation of consultation reasons and diagnoses. The most frequent consultation reasons in the MCH in 2013 were skin conditions (24%), musculoskeletal conditions (16%) and psychological disorders (14%), in GP practices these were musculoskeletal conditions (22%), conditions affecting the digestive system (14%) and skin conditions (12%). Essential (primary) hypertension, diabetes mellitus type 2 and back pain are among the top-10-diagnoses in GP practices, as well as in MCH. With regard to the other top-10-diagnoses, there are clear differences between GP practices and MCH: “Psychological behavioural disorder due to alcohol” and diagnoses in connection with trauma, skin infections and acute respiratory infections stand out in MCH. 35% of the homeless patients reported a lack of health insurance as the reason for “not making use of” the regular health care system, while 10% reported they were unable to visit a regular general practitioner due to physical or psychological reasons. In the years 2013–2020 46% to 73% of the 8.380 MCH patients had no health care insurance. Conclusion Patients consulting the MCH suffer from medical conditions typical for the homeless, namely skin diseases, wounds, injuries and behavioural disorders due to alcohol abuse, but also from “typical” symptoms in regular GP care as cough or lower back symptoms. Consultation reasons mostly are acute illnesses. Chronic diseases are equally present in regular GP and MCH patients, but pose a great challenge for the homeless among other things due to their irregular contact with the health care system. The lack of health insurance poses the greatest hurdle to the integration of the homeless into the regular health care system.