Formalin fixed and paraffin-embedded tissue specimens collected during surgery or autopsy, are an important source for retrospective diagnosis and identification purposes. Genomic DNA degradation or PCR amplification inhibition are the major cause of DNA amplification failure. Routinely, xylene is used to remove paraffin from paraffinembedded tissue sections. We tested methyl tert-butyl ether (MTBE), as an alternate organic solvent, which is less harmful for organism than xylene.Using different tissues (heart, kidney, liver) from randomly selected autopsies (n=10) we compared performance of MTBE and xylene for removal of paraffin during a preparation process compatible with automated staining equipment. All these extracted DNA samples were amplified and genotyped using human identification Identifiler multiplex.Our experiments points that there is no difference in the range of genotyped microsatellite loci, regardless MTBE or xylene dewaxing. The heart specimen has the highest number of successfully genotyped STR loci, followed by the kidney and the liver. For the genomic template above 260 base pairs of the length no products were obtain from the routinely collected autopsy material. It is worthy of note that MTBE is safer than xylene and according to the current European Community regulations no chemical fume hoods are required for MTBE handling. Thus, MTBE might be preferred to remove paraffin from tissue specimens in forensic or histopathology laboratories not equipped with systems of airborne exposure protection.