Several sperm DNA integrity and chromatin quality assays have been developed and used for the detection of sperm DNA fragmentation and chromosomal aberrations [1, 2]. The Comet assay is one of the most commonly used single cell gel electrophoresis methods first developed by Östling and Johanson [3]. Damaged or fragmented sperm DNA is separated from undamaged DNA by electrophoresis. Fluorescent in situ hybridization (FISH) is a hybridization method that provides specific identification of selected DNA sequences and is frequently used for cytogenetic analysis of spermatozoa. These two methods were combined as the Comet-FISH technique first by Santos and colleagues in 1997 [4]. The Comet-FISH technique is a combination of two well-known methods, the Comet assay and FISH, and is a useful detection tool for screening of whole and region-specific DNA damage [5, 6]. In addition, the analysis of labeled DNA sequences and whole chromosomes of interest and identification of region-specific DNA and overall damage and repair in single cells is possible [7, 8]. Therefore, the modification of these assays interpolates hybridization with specific fluorescent-labeled probes to selected DNA sequences of interest after unwinding and electrophoresis [6] and developed a standardized Comet assay for human sperm with additional information for telomeres or special DNA sequences of interest. Thus, specific gene sequences can be detected using the Comet-FISH technique [9].