OBJECTIVE. Physiological root resorption is a programmed event that takes place in primary teeth leading to elimination of all root structures. The mechanism behind pulp elimination indicates apoptosis, but its pathway has not been well characterised yet. To better understand this event, we evaluated the gene expression of bax, bcl-2, caspase-3 and caspase-8 through real-time polymerase chain reaction (PCR) and immunohistochemistry expression of Caspase-8 and Bax in pulps. METHODS. Samples were split into two groups: pulps from primary teeth with physiological root resorption (n = 40) and control (n =40), pulps from permanent teeth. Samples of each group were split into PCR (n = 20) and immunohistochemistry (n = 20). RESULTS. Pulps from primary teeth showed a higher caspase-3 mRNA level than pulps from permanent teeth. The expression of bax gene was more intense than caspase-8 but both did not show difference between groups. The bcl-2 mRNA level was incipient and similar between groups. Histopath slides did not show any evidence of inflammatory infiltration, which implies that extrinsic via is not likely to be involved. Immunohistochemistry reaction to Bax and Caspase-8 supported PCR results. CONCLUSIONS. Pulp apoptosis is likely to occur via caspase-3 activation through the mitochondrial pathway.