Microbiological contamination of retrieved tissues has become a very important topic and a critical aspect in the safety of allografts. We have analysed contamination in 11,129 tissues with a longitudinal contamination profile for each individual tissue. More specifically, 10,035 musculoskeletal tissues and 1,094 cardiovascular tissues were retrieved from a total of 763 multi-tissue donors, of whom 105 were heart-beating donors as well as organ donors, while the remaining 658 were non-heart beating donors and tissue donors only. All tissues were decontaminated twice, the first time immediately after retrieval and the second time after processing. Each tissue was submitted to microbiological culture three times, i.e., upon retrieval (Time 1), after the first decontamination (Time 2) and after the second decontamination (Time 3). The contamination rate for musculoskeletal tissues was 52%, 16.2% and 0.5% at Time 1, 2 and 3, respectively. The contamination rate for cardiovascular tissues was 84%, 42% and 6%. More than one strain was simultaneously present in 10.8% of musculoskeletal tissues and 44.6% of cardiovascular tissues. Out of 8,560 non-heart-beating donor musculoskeletal tissues, 4,689 (54.8%), 1,383 (16.2%) and 42 (0.5%) were contaminated at Time 1, Time 2 and Time 3, respectively. Out of 1,475 heart-beating donor musculoskeletal tissues, 522 (35.4%) 113 (7.7%) and 2 (0.1%) tissues were found to be contaminated at Time 1, 2 and 3, respectively. Out of 984 non-heart beating donor cardiovascular tissues, 869 (88.3%), 449 (45.6%) and 69 (7%) proved positive at Time 1, 2 and 3 respectively, while 50 (45.5%) and 10 (9.1%) heart-beating donor cardiovascular tissues were contaminated at Time 1 and 2. No tissue was contaminated at Time 3. Based on our methods, the two-step decontamination approach is mandatory in order to drastically reduce the number of tissues found to be positive at the end of the process.