Cyanoacrylate ester (CA) is commonly used by criminalists to detect latent fingerprints on smooth surfaces. We investigated whether this treatment has an influence on a subsequent DNA typing of biological stains, and on the efficiency of three different forensic PCRs (mtDNA, Y-STR determination and the Profiler Plus kit). Using fluorescence labeled primers and an automated detection system, we could show that the presence of CA led to weaker PCR products. Depending on the DNA extraction method the amplification results were significantly weaker compared to untreated controls. To simulate forensic cases we prepared blood and saliva stains on glass slides, extracted the DNA using two different methods and compared the signal intensities of the amplified DNA fragments. Depending on the extraction methods, the presence of CA significantly hampered the amplification of DNA from small stains whereas there was virtually no difference comparing the amplification results of DNA extracted from bigger stains.