The importance of complex nucleic acid samples is constantly increasing in modern genetics. Examples are genomic DNA or RNA isolated from difficult sources (e.g. Formalin Fixed Paraffin Embedded tissue samples), cDNA preparations, complex PCR and samples prepared for ChIP- or NGS sequencing. Those samples are treated according to various protocols before they are analyzed. No good methods exist to analyze quality, type, composition and size distribution of nucleic acids in such samples on different time points in the process. We have developed Two-Dimensional Strandness-Dependent Electrophoresis (2D-SDE) to analyze such samples. Using 2D-SDE, we can separate between single-stranded DNA, double-stranded DNA, RNA*DNA hybrids, crosslinked DNA and other types of DNA lesions. Our results indicate that some of those samples contain highly damaged nucleic acids that will interfere with analysis, downstream processes and reproducibility of experiments.