The measurement and evaluation of changes in calcium levels between cellular compartments can provide important information for the understanding of biochemical processes, both physiological and pathological. The objective of this study was to validate the use of the calcium diagnostic kit (Arzenazo III) to tissue samples from the Central Nervous System. We used 96-well, flat-bottomed microplates with an internal diameter of 6.7 mm, total height of 12 mm and actual height of 10.705 mm, bottom thickness 1.295 mm, to carry out the tests and calculation parameters, therefore, the path optic was 5.729 mm with a total volume of 202 µL per well. The microplates were incubated at 37 °C for 2 minutes. Optical densities were measured at 630 nm on the Elx800 plate reader, (BioTek, VT, USA). According to the Arzenazo III Bioclin© calcium diagnostic kit. the absorbance of the tests/samples was normalized with the absorbance of the blank (colorimetric reagent 2 - Arsenazo III – Arzenazo III Bioclin© calcium diagnostic kit). PFC, Thalamus and Hippocampus were normalized by blank and presented respectively 0.1782 ± 0.0013; 0.1296 ± 0.0102; 0.0231 ± 0.0053; 0.0170 ± 0.0051; 0.0136 ± 0.0026. The calculation µg calcium / mg tissue obtained 0.4670 ± 0.1056 to sample PFC; 0.4322 ± 0.1228 to sample Thalamus and 0.1027 ± 0.0203 to sample Hippocampus. Although the limitations of the technique, the measurement of free calcium in the CNS tissues (PFC, Thalamus and Hippocampus) showed positive and satisfactory results, as an alternative and viable means for the quantification of calcium levels.