Prism has been able to perform one- and two-way ANOVA for many versions, and now can also perform three-way ANOVA.

Enter your data on a grouped table like this.

Two of the factors must have only two levels (e.g. male/female; low fat/high fat), but the the third factor (designated by different rows) can have more levels (more than two rows).

The three-way ANOVA dialog is similar to the dialog for one- and two-way ANOVA, but the choices for multiple comparison goal are a bit different:

Here is a portion of the results table, showing all seven P values. Yes, seven! Three-way ANOVA is complicated.  

 

Prism 7  provides a new kind of three-way graph to display data entered into three-way ANOVA: