The present in vivo study was performed to investigate the levels of the pro-inflammatory cytokines, interleukin (IL)-1 alpha, IL-6, and IL-8, in primary molars for which pulpotomy was clinically indicated, and to evaluate the success rates of three different pulpotomy agents employed for cariously (CExp) or mechanically exposed (MExp) primary molars. Forty-seven primary molars were classified as MExp or CExp according to the type of pulpal exposure. Pulp tissue was harvested and analyzed using enzyme-linked immunosorbent assay (ELISA). Subsequently, three pulpotomy agents calcium hydroxide (CH), mineral trioxide aggregate (MTA), and formocresol (FC)-were applied randomly, and the outcome was observed radiographically for 18 months. Levels of IL-6 and IL-8 were significantly higher in CExp pulp than in MExp pulp (P < 0.05). In the CH pulpotomy group, MExp teeth showed a higher success rate than CExp teeth. There was no significant difference in success rate between MExp and CExp teeth in both the FC and MTA groups. The levels of IL-6 and IL-8 have the potential to become indicators of pulp status and can be monitored by researchers to make the prognosis of vital pulp therapies less uncertain. As MTA and FC yielded higher rates of success than CH in CExp teeth, the choice of pulpotomy agent appears to be important in this context.