The spionid polychaete Polydora sp. can live and reproduce inside the oysters' shell, excavating a U-shaped burrow the central portion of which is filled with detritus and particles of dissolved shell. The oyster responds by secreting an organic layer, confining the worm, and later covering it with calcitostracum. This process creates a characteristic "mud blister". Crassostrea gigas were analysed for the organic matrix amino acid content and 14 metals of the whole shell of normal oysters and severely Polydora infested ones. Amino acid, DOPA and FT-Raman analyses were also performed on isolated membranes from the characteristic mud blister and on prismatic layer insoluble matrix (PLIM) of infested oysters, with the aim of detecting any differences between the two organic matrices. Membranes and PLIM composition differ from whole normal shell organic matrix by having lower aspartate and glycine and higher levels of virtually all hydrophobic amino acids, especially alanine. There are no significant differences between membranes and PLIM in the ratio of charged to non-polar amino acids, respectively 0.54 and 0.59. L-DOPA content is also similar in the two matrices with 0.45 (± 0.18) and 0.57 (± 0.30) ng.mg−1 protein for PLIM and membranes respectively. The FT-Raman spectra of membranes is very similar to that of PLIM, suggesting that they have identical composition. Zinc, iron and manganese are significantly higher in infested than in normal shells. Infested oysters can provide an excellent opportunity for investigating normal biological calcification processes.