Since 2003, an epidemic of lymphogranuloma venereum (LGV) has been ongoing in men who have sex with men (MSM) in Europe. Of 92,271 MSM consulting sexually transmitted disease (STI) clinics in the Netherlands between 2006 and 2011, 63,228 (68%) were tested for anorectal Chlamydia infection, with 6,343 (10%) positive diagnoses. In 4,776 of those (75%), LGV testing was performed, with regional variation from 7% to 97%. In total 414 LGV cases were diagnosed, a mean annual positivity rate of 8.7%, decreasing from 14% in 2007 to 6% in 2011, but increasing to 13.1% during 2012 (184 new cases). Risk factors for LGV were human immunodeficiency virus (HIV) positivity (odds ratio (OR)=4.1; 95% confidence interval (CI): 3.2–5.3), STI symptoms (OR=4.1; 95% CI: 3.1–5.4), more than 50 sex partners in the past six months (OR=3.7; 95% CI: 1.1–12.4), older age (40–44 years: OR=2.1; 95% CI: 1.5–2.8), no condom use (OR=2.2; 95% CI: 1.2–3.9) and homosexuality (as opposed to bisexuality; OR=2.2; 95% CI: 1.1–4.2). Regional differences in LGV testing rates limit national LGV surveillance, leading to an underestimation of the real incidence. Characteristics of MSM with LGV did not change over time, so existing prevention strategies should be intensified.