Bixa orellana fruit extracts were studied by time-of-flight secondary ion mass spectrometry (ToF-SIMS). The intensity of the peak at m/z 396, assigned to the bixin molecular ion plus two hydrogen atoms (C25H(32)O(4+), decreased as the extract was heated and nearly disappeared with heating above 150 degrees C. Simultaneously, the formation of dimers at m/z 790, 804, and 818 was observed. The ToF-SIMS spectrum is characterized by a large amount of peaks generated by the principal ions and their multiple fragmentation patterns. To extract maximum information from the data set, multivariate statistical analysis was applied. Principal component analysis revealed important structural changes of the bixin molecule upon heating at different temperatures. This information can be used by the food industry as by controlling the temperature of the heating process the red/yellow balance of this colorant can be tuned.