Confounding is a significant challenge in endodontic research, as it can blur the true effect and relationship between exposure and outcomes, potentially compromising the internal validity of research findings. Confounding variables can create apparent differences between study groups when no actual difference exists or fail to reveal true differences when they are present. Additionally, confounding can lead to either an underestimation or an overestimation of the effect of exposure on the outcome. This narrative review aims to (i) define confounder variables and explain how to identify them, (ii) elaborate methods for controlling confounders, and (iii) discuss how confounders can obscure any causal relationship. Confounding variables can be controlled through study design such as randomization, matching and restriction, or adjusted using statistical methods like stratification and multivariable models. However, inadequate control of confounding can result in residual confounding, which poses a significant threat to the interpretation of findings in endodontic research.