In statistics, imputation is the process of replacing missing data with substituted values. When substituting for a data point, it is known as "unit imputation"; when substituting for a component of a data point, it is known as "item imputation". There are three main problems that missing data causes: missing data can introduce a substantial amount of bias, make the handling and analysis of the data more arduous, and create reductions in efficiency. Because missing data can create problems for analyzing data, imputation is seen as a way to avoid pitfalls involved with listwise deletion of cases that have missing values. That is to say, when one or more values are missing for a case, most statistical packages default to discarding any case that has a missing value, which may introduce bias or affect the representativeness of the results. Imputation preserves all cases by replacing missing data with an estimated value based on other available information. Once all missing values have been imputed, the data set can then be analysed using standard techniques for complete data. There have been many theories embraced by scientists to account for missing data but the majority of them introduce bias. A few of the well known attempts to deal with missing data include: hot deck and cold deck imputation; listwise and pairwise deletion; mean imputation; non-negative matrix factorization; regression imputation; last observation carried forward; stochastic imputation; and multiple imputation.

By far, the most common means of dealing with missing data is listwise deletion (also known as complete case), which is when all cases with a missing value are deleted. If the data are missing completely at random, then listwise deletion does not add any bias, but it does decrease the power of the analysis by decreasing the effective sample size. For example, if 1000 cases are collected but 80 have missing values, the effective sample size after listwise deletion is 920. If the cases are not missing completely at random, then listwise deletion will introduce bias because the sub-sample of cases represented by the missing data are not representative of the original sample (and if the original sample was itself a representative sample of a population, the complete cases are not representative of that population either). While listwise deletion is unbiased when the missing data is missing completely at random, this is rarely the case in actuality.

Pairwise deletion (or "available case analysis") involves deleting a case when it is missing a variable required for a particular analysis, but including that case in analyses for which all required variables are present. When pairwise deletion is used, the total N for analysis will not be consistent across parameter estimations. Because of the incomplete N values at some points in time, while still maintaining complete case comparison for other parameters, pairwise deletion can introduce impossible mathematical situations such as correlations that are over 100%.

The one advantage complete case deletion has over other methods is that it is straightforward and easy to implement. This is a large reason why complete case is the most popular method of handling missing data in spite of the many disadvantages it has.

A once-common method of imputation was hot-deck imputation where a missing value was imputed from a randomly selected similar record. The term "hot deck" dates back to the storage of data on punched cards, and indicates that the information donors come from the same dataset as the recipients. The stack of cards was "hot" because it was currently being processed.

One form of hot-deck imputation is called "last observation carried forward" (or LOCF for short), which involves sorting a dataset according to any of a number of variables, thus creating an ordered dataset. The technique then finds the first missing value and uses the cell value immediately prior to the data that are missing to impute the missing value. The process is repeated for the next cell with a missing value until all missing values have been imputed. In the common scenario in which the cases are repeated measurements of a variable for a person or other entity, this represents the belief that if a measurement is missing, the best guess is that it hasn't changed from the last time it was measured. This method is known to increase risk of increasing bias and potentially false conclusions. For this reason LOCF is not recommended for use.

Cold-deck imputation, by contrast, selects donors from another dataset. Due to advances in computer power, more sophisticated methods of imputation have generally superseded the original random and sorted hot deck imputation techniques. It is a method of replacing with response values of similar items in past surveys. It is available in surveys that measure time intervals.

Another imputation technique involves replacing any missing value with the mean of that variable for all other cases, which has the benefit of not changing the sample mean for that variable. However, mean imputation attenuates any correlations involving the variable(s) that are imputed. This is because, in cases with imputation, there is guaranteed to be no relationship between the imputed variable and any other measured variables. Thus, mean imputation has some attractive properties for univariate analysis but becomes problematic for multivariate analysis.