Archiving of clinical materials as Formalin-Fixed, Paraffin-Embedded (FFPE) samples is a common practice. However, the methods used for fixation and storage significantly damage the nucleic acids from these samples. Additionally, FFPE DNA samples are often available in only very small amounts. As a result, it can be challenging to construct high quality libraries in sufficient quantity to achieve good sequence data at the desired depth of coverage. NEBNext® Ultra™ II libraries were made from low nanogram amounts of several FFPE DNA samples of varying age and quality and then sequenced. Bioanalyzer traces of the libraries and analysis of the sequencing data show that the quality of the libraries was high.