This study aimed to identify the chemical composition resulting from the chemical interaction between calcium hypochlorite [Ca(OCl)2] and chlorhexidine (CHX) using different 1H and 13C nuclear magnetic resonance spectrometry (NMR), correlated two-dimensional spectroscopy (2D COSY), heteronuclear single quantum coherence (HSQC), and Fourier Transform Infrared Spectroscopy (FTIR) experiments. The 5.25% Ca(OCl)2 was mixed with 2% CHX in a 1:1 ratio, obtaining an orange-brown precipitate that was filtered, washed in ultrapure water, dried and characterized by 1H and 13C NMR, 2D COSY, HSQC and FTIR. One-dimensional and two-dimensional NMR spectra demonstrated the chemical changes around the protons and carbon atoms of the initial CHX and after reacted with Ca(OCl)2. These techniques and FTIR show that the interaction generated two by-products from the degradation of CHX, none of which were parachloroaniline (PCA) despite both products obtained being substituted benzene compounds. Using NMR and FTIR data together with a previously proposed catalytic cleavage degradation mechanism for CHX, the products appear to be parachlorophenylurea (PCU) and parachlorophenylguanidyl-1,6-diguanidyl-hexane (PCGH). Therefore, this in vitro study demonstrated that the precipitate formed from the chemical interaction between Ca(OCl)₂ and CHX results in two by-products, PCU and PCGH, neither of which is PCA. Due to the absence of cytotoxicity studies on the products generated from the combination of Ca(OCl)₂ and CHX, an intermediate rinse with an inert solution is recommended to remove these compounds from the root canals.