A cleaning protocol for the CryoXtract Automated Frozen Sample Aliquotter (AFSA) was tested for its effectiveness in eliminating sample-to-sample carryover during hands-free frozen sample aliquotting. The instrument's test platform was used to extract a statistically significant number of frozen cores from frozen bovine serum samples spiked with human DNA and from identical DNA-free frozen controls, processed in alternating succession, with a proprietary cleaning protocol performed in between samples. Measurements of DNA content by a highly sensitive real-time quantitative polymerase chain reaction assay revealed no traces of DNA in the frozen control cores, whereas they revealed the expected DNA amounts in all DNA-containing frozen cores. Analysis of high-copy DNA demonstrated that CryoXtract's AFSA's cleaning protocol effectively reduced DNA carryover by more than a million-fold.