MicroATX is larger than FlexATX. A typical microATX board will have up to four expansion slots (PCI, AGP and/or other types). I don't think FlexATX can have more than three. A FlexATX board should fit a FlexATX, MicroATX or regular ATX case, unless it is a fully-proprietary design or something. I think there are other differences too, such as the permitted CPU socket location. I have seen FlexATX mostly being used for BookPC's.