Changes in medical practices during transitions in regulating healthcare are rarely investigated. In this study we investigated changes in medical end-of-life decisions with a possible or certain life-shortening effect (ELDs) that occurred during the legalization process of euthanasia in Belgium. We took representative random samples from deaths reported to registries in Flanders, Belgium in 1998 (N = 3999) at the beginning of the process and in 2001 (N = 5005), at the end of the process. The reporting physicians received an anonymous mail questionnaire about possible ELDs, preceding the death involved. We found no significant shifts in epidemiology of diseases between 1998 and 2001. The overall incidence of ELDs did not change (39.3 % vs. 38.4 %). The incidence decreased for euthanasia (1.1 % vs. 0.3 %), administering life-ending drugs without patient’s explicit request (3.2 % vs. 1.5 %), and alleviation of pain and symptoms with life-shortening co-intention (5.3 % vs. 2.8 %). It increased for alleviation of pain and symptom without life-shortening intention (13.2 % vs. 19.2 %), and remained stable for non-treatment decisions (16.4 % vs. 14.6 %). All decisions in 2001 were more often discussed with patients, their relatives and nurses. In 2001, continuous deep sedation was reported in 8.3 % of deaths. We can conclude that physicians’ end-of-life practices have substantially changed during the short but tumultuous legalization process of euthanasia in Belgium. Although follow-up research is needed to investigate the continuance of these changes, it is important for policy makers to keep in mind that social factors related to transitions in healthcare regulation may play an important role in the physicians’ actual behaviour.