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What you are asking is a very involved question..there are lots of differences between between BJT and MOS, the foremost being what "darla1" said.
Further,
1) in BJT there is a static power consumption due to finite Ib(base current) whereas in MOS we can have a zero DC power, the reason for advent of MOS in first place..
2)Ic has exponential current relationship to Vbe in BJT whereas in MOS we have a square law relationship between Ids and Vgs.Thus in terms of gain we get more gain with BJT than with MOS.However, the exponential characteristic causes BJT to be more non linear than MOS.
there are many more differences and i suggest you to google with "BJT vs. MOS" keywords...
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