Human calcium phosphate calculi: two sialoliths, a urolith, a rhinolith, and a tonsillolith were investigated by scanning electron microscopy (SEM) and energy-dispersive X-ray analysis (EDX). The sialoliths and urolith had appositional shells with thick cortices, respectively, around several nuclei composed of calcospherulites and a rubber-film fragment. The rhinolith had a thin cortex with appositional laminations around a glomerulus-like mass of calcified cotton-like strings. The tonsillolith had a rough cortex with appositional laminations. Its porous interior was composed of numerous calcified conglomerates with microorganisms and calcified masses with fine appositional laminations around the conglomerates. The major crystals were identified as biological apatites (AP) with a sand-grain rather than a needle-like shape, and plate-shaped octacalcium phosphate (OCP). The AP deposits of the rhinolith probably were associated with magnesium (Mg) phosphates or contained Mg. No OCP was found in the rhinolith. The AP deposits were mainly formed by extracellular calcification. Hexahedral crystals, identified as Mg-containing whitlockite (WH), were precipitated in the internal spaces of the AP and OCP deposits. The rhinolith nucleus consisted of WH crystal deposits only.