The compositions of both organic and mineral parts of shells of Nautilus macromphalus, a Cenozoic nautiloid and Jurassic ammonites are compared. The microstructures of the fossil shells show minor diagenetic changes, despite their aragonitic mineralogy. The bulk analysis of the organic matrices, molecular weights, acidity and amino-acid contents have been studied. All the fossil shells are compositionally altered relative to modern counterparts, with the organic components both extensively lost and chemically modified. Alterations are variable within a single fossil site. Implications of these diagenetic changes for palaeoenvironmental reconstructions are examined.