In chronic lymphocytic leukemia, mutations and deletion of chromosome 17p are well-characterized biomarkers associated with poor progression-free and overall survival following chemoimmunotherapy. Patients harboring low burden mutations with variant allele frequencies of 0.3-15% have been shown to have similar dismal outcome as those with high burden mutations. We here describe a highly sensitive deep targeted next-generation sequencing assay allowing for the detection of mutations as low as 0.2% variant allele frequency. Within a consecutive, single center cohort of 290 newly diagnosed patients with chronic lymphocytic leukemia, deletion of chromosome 17p was the only aberration significantly associated with shorter overall survival and treatment-free survival. We were unable to demonstrate any impact of mutations, whether high burden (variant allele frequency >10%) or low burden (variant allele frequency ≤10%), in the absence of deletion of chromosome 17p. In addition, the impact of high burden aberration (deletion of chromosome 17p and/or mutation with variant allele frequency >10%) was only evident for patients with IGHV unmutated status; no impact of aberrations on outcome was seen for patients with IGHV mutated status. In 61 patients at time of treatment, the prognostic impact of mutations over 1% variant allele frequency could be confirmed. This study furthers the identification of a clinical significant limit of detection for robust mutation analysis in chronic lymphocytic leukemia. Multicenter studies are needed for validation of ultra-sensitive mutation assays in order to define and implement a technical as well as a clinical lower limit of detection.