The authors describe a colorimetric method for highly selective determination of cystamine using silver nanoparticles capped with thiomalic acid (TMA-AgNPs). The TMA-AgNPs exhibit a strong surface plasmon resonance absorption band at 395 nm. After the addition of cystamine to their yellow colloidal solution, the absorption maximum at 395 nm decreases gradually, and a new absorption peak appears at around 560 nm. This is accompanied by a color change, first to green and then to purple. The aggregation of NPs induced by cystamine is assumed to be due to the electrostatic interaction between capped NPs and cystamine. Aggregation was confirmed by UV–vis absorptiometry and transmission electron microscopy. A linear correlation was obtained between the ratio of absorbances at 560 and 395 nm and the cystamine concentration in the range between 0.2 μM and 10.0 μM. The limit of detection is 46 nM. The method was successfully applied to the determination of cystamine in spiked human serum and urine samples. Recoveries ranged between 94.0 % and 100.9 %, and relative standard deviations are <9.50 % (for n = 3).