Causal inference is the process of determining the independent, actual effect of a particular phenomenon that is a component of a larger system. The main difference between causal inference and inference of association is that causal inference analyzes the response of an effect variable when a cause of the effect variable is changed. The study of why things occur is called etiology, and can be described using the language of scientific causal notation. Causal inference is said to provide the evidence of causality theorized by causal reasoning.

Causal inference is widely studied across all sciences. Several innovations in the development and implementation of methodology designed to determine causality have proliferated in recent decades. Causal inference remains especially difficult where experimentation is difficult or impossible, which is common throughout most sciences.

The approaches to causal inference are broadly applicable across all types of scientific disciplines, and many methods of causal inference that were designed for certain disciplines have found use in other disciplines. This article outlines the basic process behind causal inference and details some of the more conventional tests used across different disciplines; however, this should not be mistaken as a suggestion that these methods apply only to those disciplines, merely that they are the most commonly used in that discipline.

Causal inference is difficult to perform and there is significant debate amongst scientists about the proper way to determine causality. Despite other innovations, there remain concerns of misattribution by scientists of correlative results as causal, of the usage of incorrect methodologies by scientists, and of deliberate manipulation by scientists of analytical results in order to obtain statistically significant estimates. Particular concern is raised in the use of regression models, especially linear regression models.

Inferring the cause of something has been described as:

Causal inference is conducted via the study of systems where the measure of one variable is suspected to affect the measure of another. Causal inference is conducted with regard to the scientific method. The first step of causal inference is to formulate a falsifiable null hypothesis, which is subsequently tested with statistical methods. Frequentist statistical inference is the use of statistical methods to determine the probability that the data occur under the null hypothesis by chance; Bayesian inference is used to determine the effect of an independent variable. Statistical inference is generally used to determine the difference between variations in the original data that are random variation or the effect of a well-specified causal mechanism. Notably, correlation does not imply causation, so the study of causality is as concerned with the study of potential causal mechanisms as it is with variation amongst the data. ^{[citation needed]} A frequently sought after standard of causal inference is an experiment wherein treatment is randomly assigned but all other confounding factors are held constant. Most of the efforts in causal inference are in the attempt to replicate experimental conditions.

Epidemiological studies employ different epidemiological methods of collecting and measuring evidence of risk factors and effect and different ways of measuring association between the two. Results of a 2020 review of methods for causal inference found that using existing literature for clinical training programs can be challenging. This is because published articles often assume an advanced technical background, they may be written from multiple statistical, epidemiological, computer science, or philosophical perspectives, methodological approaches continue to expand rapidly, and many aspects of causal inference receive limited coverage.

Common frameworks for causal inference include the causal pie model (component-cause), Pearl's structural causal model (causal diagram + do-calculus), structural equation modeling, and Rubin causal model (potential-outcome), which are often used in areas such as social sciences and epidemiology.