In order to minimize the incidence of local and/or systemic side effects, the biocompatibility of all endodontic materials should be investigated by various in vitro and in vivo tests prior to clinical application. The battery of in vitro tests includes determinations of mutagenicity, cytotoxicity, and antibacterial effects. Several reports have shown that paraformaldehyde-containing ZnO-eugenol cements in particular, such as Endomethasone and N2, are antibacterial. On the other hand, it has been found that endodontic materials with strong antimicrobial activity are frequently mutagenic, i.e., primarily those which release formaldehyde. Cell culture tests clearly show significantly different cytocompatibility of the various types of endodontic sealers: in general, formaldehyde-containing ZnO-eugenol cements are classified as highly/extremely cytotoxic, whereas most Ca(OH)2-based sealers are rated as possessing good or excellent cytocompatibility. These results were confirmed by numerous histological studies in vivo. Sealers with inferior biocompatibility, such as formaldehyde-releasing materials, should no longer be applied in practice because safer alternatives are available.