Abstract Background Little is known about the healthcare needs of the increasing number of undocumented migrants in Europe. We aimed to gain knowledge about undocumented migrants use of a free healthcare clinic including an outreach programme in Denmark. Methods We conducted a retrospective cohort study of all patients registered in the database at the AmiAmi healthcare clinic in Fredericia, Denmark, 1 January 2006–30 July 2019. Results In all, 579 patients from 47 different countries were included, of which 525 (90.7%) were cis-women (= assigned female sex at birth and identifies as female). They had a total of 3135 consultations (median 3, interquartile range 2–6), and 19% used the clinic over a period of >2 years. In all, 820 consultations (26%) were done as part of the outreach programme, and the number of outreach contacts increased significantly over the study period (P < 0.001). Of 738 tests for sexually transmitted infections (STIs), 76 (13.1%) patients were found positive for one or several STIs. Transgender women and cross-dressing men had significantly higher risk of STIs (25.8% vs 10.3%, P = 0.007) compared with cis-women. Of 94 patients referred to the public healthcare system, the majority (n = 64) was referred to the department of gynaecology during pregnancy or for induced abortion. A total of 52 patients (9.0%) reported being submitted to abuse or violence while in Denmark, and another 24 (4.1%) were registered as victims of human trafficking. Conclusions Our results highlight the multifaceted healthcare needs of undocumented migrants, with an increasing use of healthcare services over the study period. It underlines the importance of outreach programmes to reach this patient group at their place of work or stay. Finally, it emphasizes that transgender female and cross-dressing male sex workers are an especially vulnerable group with higher risk of human immunodeficiency virus and other STIs compared with cis-women.