While large manufacturers are free to build PCs in whatever shape they desire, ATX and its derivatives dominate the do-it-yourself market. Smaller variations of ATX limit the room you have for expansion and make you more reliant on integrated or external devices, while allowing compact system dimensions. Even as advancements in on-board audio and network controllers have improved those subsystems to the point where you don't need add-in cards with those capabilities, on-die graphics are still fairly anemic. Unless you're only performing productivity tasks and watching video on your PC, you'll probably want a discrete card for 3D tasks. While office systems and media players may serve a fixed role throughout their useful lives, it's a good idea to have at least some room for expansion cards when building a multipurpose configuration.
ATX Through Mini-ITX
ATX was designed to address three major shortcomings of the earlier AT form factor, and it offers a few minor improvements as well. First, a designated portion of the board for the CPU socket keeps it out of the way of long cards, where AT boards had the CPU mounted behind or in place of card slots. Second, the inclusion of an I/O panel on the motherboard itself negates the need for slot brackets to break out common connections like USB, Ethernet, and audio. Third, a cooling path from the lower-front to the upper-rear of the case vents heated air through the power supply and/or an exhaust fan. All three major advancements are centered on splitting the board between the expansion and CPU areas.
Most significant of the more minor improvements was the addition of a power switch on the motherboard, rather than the power supply. This allowed the system to turn itself off at shutdown, and made possible features like wake-on-ring (using a modem), wake-on-LAN (using a network adapter), timed power up/power down, and keyboard power-on hot-buttons.
ATX derivatives are based on the same CPU section, so that smaller motherboards are able to fit into larger cases if desired. ATX standards include microATX and FlexATX. Most Shuttle-style PC cubes (often called SFF for Shuttle Form Factor or Small Form Factor) use a two-slot variation of the FlexATX form factor cut to approximately eight inches, and VIA further shortened its mini-ITX form factor to 6.75 inches by reducing the maximum slot count to one.
ATX size specifications are based on fractional inches, and rounding to the nearest millimeter is the most likely reason why the mounting holes of many motherboards are slightly misaligned with the mounting points of many cases. Even the originator of ATX, Intel, rounds the dimensions of recent specification updates when converting from original inch designations.

The image above compares the maximum size and maximum number of slots allowed on various ATX-based form factors, with dashed lines indicating how the mounting holes in smaller boards still align with those of larger cases. It also shows a long-forgotten solution to the problems of mini-ITX.
Before there were any high-performance products based on the mini-ITX form factor, AMD attempted to standardize Shuttle-style gaming cubes with a newer specification called DTX. Its single-slot derivative, mini-DTX, resembles mini-ITX except that it’s deeper, which makes room for four memory modules and a full-sized CPU voltage regulator. While most mini-ITX-optimized gaming cases are designed to hold a DTX motherboard, persistence of the mini-ITX moniker has prevented motherboard makers from taking advantage of the extra depth. As shown above, the same rule of “smaller motherboard fits larger case” applies.
Over The Top (Or Under The Bottom)
Oversized motherboards have existed for as long as any of the form factors mentioned above. One of the oldest is EATX, with its 13” depth (front to rear). Foxconn’s attempt to develop a 10-slot form factor succeeded only in introducing 10-slot cases to the market, and other manufacturers responded to the new cases by producing nine-slot-tall (13.6”) XL-ATX motherboards that can use the case’s tenth slot to hold a thick graphics card in the platform's bottom slot. The associated cases are specified as XL-ATX-compatible, and they'll still hold a full range of smaller boards down to mini-ITX.

Does the mobo have enough pci-e x16 slots
Does the mobo have the right chipset for the cpu
Does the mobo have enough ram sockets
Enough for your 'beginner'
[EDIT]
I suppose perhaps you might need to ensure form factor is correct.