Crosstabs expects the raw data as vectors, if you only have counts you will need to expand your data into vectors, for instance X would equal 1 for disease and 2 for no disease and Y would equal 1 for experimental condition and 2 for control condition.
If you just have the counts or don't want the hassle of expanding your data to vectors you could look at using a Fisher's exact test instead:
x = table([1;2],[3;4],'VariableNames',{'Experimental','Control'},'RowNames',{'Disease','NoDisease'})
I tend to use Fischer's test instead because it is more relaible with small sample sizes.
Alternatively you could look at some files on the file exchange like this one:
Or if I just want a one off calculation I will often use online contingency table calculators instead (not Matlab?! the shock, the horror!):
Hope this helps.
