Objective: To estimate the screening rates for hepatitis C (anti-HCV antibodies) and hepatitis B (HBs antigen) in 2016 at the national, regional, and—for the first time—departmental levels, and to compare these indicators with those estimated in the two previous surveys. Methods: The 2016 LaboHep survey was conducted retrospectively in 2017 among a random sample of clinical laboratories. The number of anti-HCV antibody and HBsAg tests, the number of tests confirmed positive for the first time in the CLS, as well as the sex and age of individuals confirmed positive, were collected. Estimates were calculated taking into account the sampling plan and after adjustment for CLS activity. Results: In 2016, 4.1 million [95% CI: 3.9–4.4] anti-HCV tests and 4.3 million [4.0–4.6] HBsAg tests were performed in France, representing a continuous increase compared to 2010 and 2013. The number of confirmed positive anti-HCV tests (45 per 100,000 inhabitants) and the anti-HCV antibody positivity rate (0.7%) were lower than in 2013 (49 per 100,000 inhabitants and 0.9%, respectively). The number of confirmed positive HBsAg tests (51 per 100,000 inhabitants) and the HBsAg positivity rate (0.8%) remained stable. Conclusion: LaboHep 2016 shows that hepatitis B and C screening activity in France continued to increase compared to previous years. The survey provided departmental-level data. These estimates are useful for guiding and measuring the impact of the screening strategy.