The predictive value of factor V Leiden and the G20210A prothrombin mutation regarding recurrent venous thromboembolism (VTE) is limited and does not influence subsequent patient management. Systematic testing for such genetic thrombophilia should be avoided, but to which extent such testing is practiced in a Swiss Hospital is unknown. To examine the current practice of factor V Leiden and/or G20210A prothrombin mutation testing in a University Hospital, and to assess the clinical consequences of testing on patients. 1388 adult patients (48.7% women) with a main diagnosis of VTE hospitalized at the Lausanne university hospital between January 2013 and December 2015. FV Leiden and/or prothrombin G20210A mutation testing was performed in 61 (4.4%) patients with VTE, an average of 20 patients/year. On multivariable analysis, age < 65 years [odds ratio and (95% confidence interval) 5.91 (3.12-11.19)], being admitted in a medical ward [5.71 (2.02-16.16)] and staying in the intensive care unit [0.34 (0.12-0.97)] were associated with thrombophilia testing. No differences were found between patients with and without testing regarding in-hospital mortality [OR and 95% CI for tested vs. non-tested: 0.23 (0.03-1.73), p = 0.153] and length of stay (multivariable adjusted average ± standard error: 16.9 ± 3.3 vs. 20.0 ± 0.7 days for tested and non-tested patients, respectively, p = 0.875). Thrombophilia testing in hospitalized patients with a main diagnosis of VTE is seldom performed. FV Leiden and/or prothrombin G20210A mutation should not be routinely assessed in patients with acute VTE.