Formalin-fixed paraffin-embedded (FFPE) tissue blocks are commonly used in the field of pathology and forensic pathology as a source of histological slides. For postmortem kinship analysis or identification, DNA can be extracted from blocks with specialized kits. However, when an STR profile should be generated from single microscope slides, the removal of the coverslip and the limited sample size poses unique challenges. We aimed to test the effectivity of agitated xylene incubation to dissolve the mounting material to facilitate the coverslip removal. DNA extraction tests were performed on 5- to 7-year-old histological slides. Xylol was used to dissolve the mounting medium to facilitate cover slide removal, one set of samples was shaken during incubation, and the other set was left still. It was found that shaking the sample while bathed in xylol decreased the incubation time from three days to two days. Agitation not just reduced the processing time but increased the quality of acquired STR profiles: on average 30% more alleles were detected from the shaken samples compared to the still bathed ones.