Background To assess the clinical variables that effect progression in patients with viable tumor after post-chemotherapy lymph node dissection due to disseminated non-seminomatous germ-cell tumors. Methods We performed a retrospective analysis of 32 patients with viable tumor after PC-RPLND, operated between 1990 and 2016. Patients were categorized into 2 groups as favorable and non-favorable (intermedia and poor) according to International Germ Cell Consensus Classification (IGCCC). Tumor size was determined as the largest dimension of retroperitoneal mass. Clinical factors and adjuvant chemotherapy were evaluated to impact on recurrence free survival (RFS) and overall survival (OS). Results The median age of the patients and follow-up duration were 28.5 (17-51) years and 51.5 (4-253) months, respectively. 5-year RFS and OS were 57.8-66.8%, respectively. On univariate analysis, percentage of viable tumor, IGCCC risk group, primary site, second-line chemotherapy and surgical margin status were significant for RFS (p = 0.034,p = 0.002,p < 0.001,p = 0.011 andp < 0.001, respectively), while IGCCC risk group, second-line chemotherapy and surgical margin status were significant for OS (p = 0.004,p = 0.010 andp < 0.001, respectively). On multivariate analysis, second-line chemotherapy and surgical margin were independent risk factors for RFS (p = 0.016, HR 4.927 95% CI 1.34-18.02 andp < 0.001, OR 9.147 95% CI 2.61-31.98, respectively) and surgical margin status was the only predictor of OS (p = 0.038, HR 3.874 95% CI 1.07-13.69). Conclusion Retroperitoneal lymph node dissection with negative surgical margin is essential for patients with viable residual tumor after chemotherapy. Need for second-line chemotherapy shows risk of progression.