The secondary ion mass spectrometry (SIMS) microscope is able to map chemical elements in tissue sections. Although absolute quantification of an element remains difficult, a relative quantitative approach is possible for soft tissue by using carbon (12C) as an internal reference present at large homogeneous and constant concentration in specimen and embedding resin. In this study, this approach is used to standardize the signal of an SIMS microscope for the quantification of halogens (9F-, 35Cl- and 79Br-) and calcium (40Ca+). Standard preparation was determined based on homogeneity and stability criteria by molecular incorporation (halogens) or mixing (calcium) in methacrylate resin. Standard measurements were performed by depth analysis on areas of 8 microns (halogens) and 150 microns (calcium) in diameter for 10-30 min, under Cs+ (halogens) or Ox+ (calcium) bombardment. Results obtained from 100-120 measurements for each standard dilution show that the relationship between the signal intensity measured and the elemental concentration (micrograms/mg of wet tissue or mM) is linear in the range of biological concentrations. This quantitative approach was applied firstly to bromine of the 5-bromo-2'-deoxyuridine (BrdU) used as nuclear marker of rat hepatocytes in proliferation. The second model concerns depletion of calcium concentration in cortical compartment in Paramecium tetraurelia during exocytosis. Then signal standardization in SIMS microscopy allows us to correlate quantitative results with those obtained from other methods.