In Denmark, eradication treatment is recommended for methicillin-resistant Staphylococcus aureus (MRSA) carriers. Here, we analyze factors associated with eradication outcome. MRSA carriers referred to the MRSA Knowledge Center at Hvidovre Hospital in 2013 were included. Carriers were sampled from nose, throat, and perineum. Eradication regimen was 5 days of mupirocin nasal ointment and chlorhexidine whole-body wash. Oral antibiotics were sometimes added. Factors associated with eradication after the first eradication attempt were analyzed by logistic regression and expressed as odds ratio (OR) with 95% confidence interval (95% CI). Of 164 individuals, 143 completed 1- and 6-month follow-up after 1st treatment. Eradication was achieved in 63 (38.4%) patients after one treatment and 101 (61.6%) individuals became MRSA free after up to 4 eradication treatments. Throat carriage was associated with a higher failure rate (OR 0.29 (0.10–0.80)), while the presence of Panton-Valentine leukocidin (PVL) genes (37%) was associated with higher success rate (OR 3.52 (1.44–8.57)). Other factors analyzed were not significantly associated with eradication outcome. None of the 26 patients lost to follow-up developed later MRSA infections. This study estimates the efficacy of treatment of MRSA carriage with an eradication rate of 38.4% after the first treatment and a total eradication rate of 61.6% after several treatments. Throat carriers had a lower eradication success rate. Adding oral antibiotics to the first treatment did not increase success. The finding of a significant higher success rate when having a PVL-positive clone should be further investigated.