Clinical endometritis (CE) is common in post-partum dairy cows and is associated with impaired reproductive performance. The aim of the study was to evaluate the effect of subclinical endometritis (SE) in cows clinically cured of CE on their fertility. The study was performed on 215 Holstein Friesian cows with CE diagnosed by vaginoscopy and ultrasound between 21 and 28 days after parturition. All cows were clinically examined three times at an interval of 2 weeks. Cows without signs of CE were considered cured, and endometrial samples from the uteri were collected by cytobrush to diagnose SE using cytological evaluation of polymorphonuclear neutrophils (PMNs) percentage. The threshold for SE was set at ≥ 5% PMNs. Intervals calving to oestrus and calving to conception, first AI pregnancy rate, pregnancy rate 200 days after artificial insemination (AI), the number of AI per pregnancy (AI/P), pregnancy loss, and culling rate were calculated. SE was diagnosed in 40.9% of cows clinically cured of CE. There were significant differences in the AI/P (3.2 vs. 2.6; p < 0.027) and the pregnancy loss (18.2% vs. 4.7%; p < 0.002) between cows with SE and without SE. Cows with SE showed a tendency towards longer interval calving to conception, lower pregnancy rate 200 days after AI, and higher culling rate. In conclusion, SE after a clinical cure of CE may reduce fertility in dairy cows.