During standard registration of incoming surgery specimens, loss of registration numbers may occur. In our laboratory two series of small bladder biopsies (numbered I–V and I–VI, respectively), obtained from two patients, were given the same laboratory registration number. The biopsies were of similar size and embedded in paraffin. Thus, five pairs of Roman-numbered paraffin blocks had the same laboratory registration numbers. The histological findings in several biopsies were similar, some showing carcinoma in situ. Only from biopsy number VI was the identity retained, and this specimen could be used as a reference. We used polymerase chain reaction (PCR)-driven microsatellite marker analysis to identify the specimens using five different microsatellite markers. Within 48 h, two different banding patterns were revealed, allowing us to distinguish the two series. In addition, in one biopsy which showed carcinoma in situ of the bladder, microsatellite instability was observed while in none of this patient's other biopsies containing carcinoma in situ could this phenomenon be detected, which may indicate intratumor heterogeneity or multifocality. In conclusion, it is possible to solve the problem of mixing up small paraffin-embedded biopsies by using microsatellite marker PCR.