This dataset belongs to the manuscript titled "Two decades of living with Echinococcus multilocularis: a clinical epidemiology study on human alveolar echinococcosis in Hungary". The manuscript has not been submitted to publication. The dataset contains a comprehensive README file (see 00_README_HAE.txt), a dataset of 40 HAE cases (see 01_Csulak_clinical_epi_data.csv), results of statistical analysis on the dataset (see 02_diagnostic_delay.pdf, 03_disease_outcome.pdf, 04_surgery.pdf, 05_ABZ_treatment.pdf, 06_ordinal_regression_model.pdf), diagrams of statistical calculations (see 07_Fig3_diagnostic_delay.jpg, 08_Fig4_disease_outcome.jpg, 09_Fig5_surgery.jpg, 10_Fig6_ABZ_treatment.jpg), and Figures of the manuscript (see 11_Fig1_HAE_MRI.jpg and 12_Fig2_histopathology_protoscoleces.jpg). Key summary points of the study Why carry out this study? Human alveolar echinococcosis (HAE) emerged in Hungary in the early 2000s. An unusual case number increase was experienced after 2018, when a comprehensive study was carried out on the epidemiology of HAE. We hypothesised that the conspicuous trend change was due to the improved disease awareness within the healthcare system, though neither the rising epidemiological risk could be excluded. What was learned from the study? The statistical model proved that the performance of the healthcare system improved; however, a lot of advanced-stage patients entered the healthcare system in both periods (before and after 2018). Knowledge dissemination campaigns could enhance the knowledge, attitude, and practice of the public, thus efficiency of prevention. A non-significant increase in case numbers was experienced in the southwestern region, which might have also contributed to the trend change of HAE. Ethical approval number: 07-03-2024/BM/2130-3/2024 (Committee for Scientific and Research Ethics of the Medical Research Council) Patients participating in this research were asked to provide informed consent before entering the study. Balázs Dezsényi (dezsenyi.balazs@semmelweis.hu), the principal investigator of the recent, authorised multicentric study, was responsible for ensuring the ethical use of patients’ data. Concerning research ethics, the form of informed consent, and the ethical use of patients’ data, Balázs Dezsényi can provide additional information.