Complex karyotype (CK) typically involves various, often extensive numerical and structural chromosomal abnormalities. In chronic lymphocytic leukemia (CLL), it represents an established adverse prognostic marker. Common methods to detect CK include classical cytogenetics and genomic microarray, however, their resolution is limited. We aimed to explore the ability of long-read sequencing for the precise characterization of complex genomic variants in CLL patient samples. CK cases were identified and characterized using classical (IL-2/CpG-stimulated chromosomal banding) and molecular (24×Cyte Multicolor FISH, CytoScan HD Array) cytogenomics. For long-read sequencing, high molecular weight DNA was isolated using chloroform-isopropanol extraction, fragmented by needle shearing, and short DNA fragments were eliminated. The sequencing libraries were prepared using the Ligation Sequencing Kit (Oxford Nanopore Technologies) and sequenced on the MinION or PromethION platform. Reads were aligned to the hg38 human genome reference, and breakpoints were identified with the SVIM variant caller.