Background Genotyping of mice is a common procedure in animal facilities. The aim of this study was to compare the quantity and quality of DNA extracted from samples obtained from young mice (YM; 10 d old) and adult mice (AM; 12 weeks old). We collected samples from the tail and ear of YM and AM. We also sampled blood, check cells (via buccal swabs), hair and fecal pellets of AM, and biopsied distal phalanx of YM. We isolated DNA using commercial kits and determined concentrations and purity by spectrophotometry. The integrity of DNA was evaluated by agarose-gel electrophoresis and polymerase chain reaction (PCR). Results DNA in all samples was amplified successfully but the intensities of bands after electrophoresis was heterogeneous. In general, tissues from YM yielded more DNA than those from AM, with differences being statistically significant for ear samples (38 ± 12 ng/μL for YM; 7 ± 3 ng/μL for AM; P = 0.006). In YM, the most DNA was obtained from ear and tail samples, with differences from the amounts obtained from phalanx samples being statistically significant (P = 0.02 and P = 0.005, respectively). In AM, the most DNA was obtained from tail and blood samples. Samples obtained by non-invasive sampling methods in adults resulted in a deficient DNA extraction. Conclusions The results of the present study do not support the previous recommendations for using non-invasive methods to genotype adult animals. The use of newborn tissue samples showed the highest efficiency for DNA extraction.