Kawaguchi, Koch, and Wang (2011) provide methodology and applications for a stratified Mann-Whitney estimator that addresses the same comparison between two randomized groups for a strictly ordinal response variable as the van Elteren test statistic for randomized clinical trials with strata. The sanon package provides the implementation of the method within the R programming environment. The usage of sanon is illustrated with five examples. The first example is a randomized clinical trial with eight strata and a univariate ordinal response variable. The second example is a randomized clinical trial with four strata, two covariables, and four ordinal response variables. The third example is a crossover design randomized clinical trial with two strata, one covariable, and two ordinal response variables. The fourth example is a randomized clinical trial with seven strata (which are managed as a categorical covariable), three ordinal covariables with missing values, and three ordinal response variables with missing values. The fifth example is a randomized clinical trial with six strata, a categorical covariable with three levels, and three ordinal response variables with missing values.