Marine calcifiers, such as clam shells, foraminifera and also cultured pearls are natural organic-inorganic nano-composite materials formed by organisms through mechanisms that are still almost entirely unknown. Despite this, they are routinely used for environmental and paleo-climatological reconstructions by relating their chemical composition to that of inorganic carbonates. Complications encountered by this methodology are often attributed to ill-defined physiological control of the organism on the mineralization of the shell, lumped together under the term ‘vital effects’. Studying the inorganic-organic building plan of marine calcifiers and some of their natural products (pearls) using a suite of state-of-the-art micro-analytical methods highlights the complicated structure and allows insight into formation mechanisms.