Research problems that require a non-parametric analysis of multifactor designs with repeated measures arise in the behavioural sciences. There is, however, a lack of available procedures in commonly used statistical packages. In the present study, a generalization of the aligned rank test for the two-way interaction is proposed for the analysis of the typical sources of variation in a three-way analysis of variance (ANOVA) with repeated measures. It can be implemented in the usual statistical packages. Its statistical properties are tested by using simulation methods with two sample sizes (n = 30 and n = 10) and three distributions (normal, exponential and double exponential). Results indicate substantial increases in power for non-normal distributions in comparison with the usual parametric tests. Similar levels of Type I error for both parametric and aligned rank ANOVA were obtained with non-normal distributions and large sample sizes. Degrees-of-freedom adjustments for Type I error control in small samples are proposed. The procedure is applied to a case study with 30 participants per group where it detects gender differences in linguistic abilities in blind children not shown previously by other methods.