Cell-free DNA (cfDNA) is small short double stranded molecule that is also found in seminal fluid. It is a product of apoptotic cells in different developmental stages during spermatogenesis. To final concentration of total cfDNA in semen contributes also cfDNA secreted from living cells and cfDNA that is result of different diseases e.g. prostate cancer or infertility. Amended concentration (high or low) can be connected to prostate cancer or male infertility and can represent important non-invasive diagnostic biomarker for detection and prognosis of these pathological conditions. In this paper, I will discuss different approaches for isolation of cfDNA from seminal fluid, which includes selection of the samples, separation, isolation, extraction, purification and analysis. Today's most popular approach for isolation is the use of commercial kits based on selective binding and elution on silica-membrane technology, magnetic-bead technology or extraction with organic solvents and salting out procedure. Furthermore I will present that I tried to isolate cfDNA from semen with QIAamp DNA Mini Kit to confirm the presence of cell-free DNA in our samples. In the end I will describe problems we are facing during cfDNA measurement which are mainly associated with low concentration of cfDNA in samples.