It's not entirely clear to me how you want C to look. The number of rows should of course be the same, but what about the length of the rows? I assume the number of common elements will vary between rows. Depending on what you want, cells could be te solution:
A = [1 2 3; 4 5 6; 7 8 9; 10 11 12];
B = [3 2 4; 4 4 6; 6 7 8; 13 14 15];
C = cell(3,1);
for i = 1:size(A,1)
C{i} = intersect(A(i,:),B(i,:));
end
If this is not what you're looking for, please try to be more specific.
