EDTA binds ca++ strongly.  

Many proteins require Ca++ as a co-factor.

Heparin interacts, i.e. through antithrombin and as such affects a whole cascade of proteins involved in blood coagulation.

To make matters more difficult: Ca++ is also an important co-factor in coagulation.

So no universal answer can be given except:  "it depends ......" on what you intend to do further on.....

Hi Nagarjuna, what do mean by "which is best"?

Both heparin and EDTA are common anticoagulants and both are used in plasma separation of whole blood.

If you are looking at specific proteins in plasma, then I agree with Judocus: "it depends..."  

It really does depends on what you want to measure afterwards. EDTA and citrate remove calcium, which most coagulation factors need. Heparin activates antithrombin thereby inhibiting coagulation by inhibiting thrombin. Heparin bound to AT also inhibits FXa. 

EDTA is most often used when you want to do hematological tests (red and white blood cell count, Hb, blood group), citrate for example damages cells so won't we useful.  

Heparin is used for clinical chemistry tests such as cholesterol, CRP, hormones etc. It interferes with PCR, so if you want to do that use EDTA.

Citrate is used when you want to do coagulation tests, because it's effect is relatively easy to reverse by adding Ca2+. EDTA and heparin influences tests such as the PT and APTT (are prolonged using those anticoagulants), and FV, VIII, Protein C and S, VWF, D-dimer  measurements. Making it difficult to interpret the results.