The main difference between eukaryotic cells and prokaryotic cells is their nucleus. 

"The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried."

Prokarytotic cells lack a membrane-bound nucleus. These cells have few internal structures that are distinguishable under a microscope. Two kinds of prokarytoic cells are bacteria and cyanobacteria.  Examples of eukarytoic cells are plants and animals.  

A second difference between eukaryotic and prokaryotic cells is thier size. Eukaryotic cells are much larger then prokaryotic cells.

A third difference between the two types of cells are their replication processes.  "Instead of going through elaborate replication processes like eukaryotes (mitosis and meiosis), bacterial cells divide by binary fission."