*Purpose: Recellularization is considered to be a potential way to solve the problem of organ shortage for transplantation. One of the conditions for the use of organs created in de- and recellularization processes is their low immunogenicity combined with low content of residual DNA. Unfortunately, the removal of residual DNA requires an aggressive decellularization protocol that causes destruction of the ECM structure, which can lead to the loss of its unique properties. The aim of our study was to compare decellularization protocols affecting residual DNA concentration and ECM damage.

*Methods: We performed 16 porcine slaughterhouse harvested pancreas decellularization procedures using Triton X-100 as a detergent agent. Decellularization protocols varied in detergent pressure and volume, time of processing , dilution agent, temperature and pH. Resulting residual DNA was tested using PicoGreen assay. ECM structure was evaluated using standard microscopy, immunofluorescence, SEM and mass spectrometry.

*Results: High pressure and high volume decellularization protocol is associated with lower residual DNA concentration but it leads to the ECM structure damage.

*Conclusions: Optimization of the detergent flow conditions during decellularization is crucial to obtain the minimum concentration of residual DNA with possible intact ECM structure. Microscopy analysis of ECM should be considered a standard element in the assessment of the scaffold before recellularization.

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