They are essentially the same thing, PFA is the polymer of formaldehyde. 

In terms of fixation, PFA does not have any fixative effect, it needs to be heated and broken down to formaldehyde for fixing tissues.

After formaldehyde fixation, you would need to perform antigen retrieval to 'undo' the cross-linked proteins, essentially exposing the epitope of  your antigen again.

Abcam has a nice page on different antigen retrieval techniques (http://www.abcam.com/protocols/ihc-antigen-retrieval-protocol), definitely try most of them out (although EDTA + protease is my prefered technique). 

They are essentially the same thing. PFA is a polymer of formaldehyde and a very pure substance if kept refrigerated. If you either depolymerize PFA in warm water in a neutral pH or resolve formaldehyde in water you would end up with formalin (aquious formaldehyde). Unfortunately formalin is not a stable solution since formaldehyde is a reletivly reactive substance and will react with itself to polymerize, or be oxidized into methanol and formic acid. For this reason commercial formalin soln. generally contain stabilizers and some level of methanol, or are contained under inert gass in a glass vial. When you want to reduce tissue auto-fluorescence then you will want to make fresh formalin from PFA. It may also help to reduce aldehyde tales and polymers with sodium borohydride after fixing. 

I wanted to correct something in Justin's answer above. Formalin is not aqueous formaldehyde. Formalin is a commercial name given a long time ago to a proprietary formulation of formaldehyde and stabilizers, but which over time has become common parlance.  Formalin sold commercially always contains stabilizers like methanol, so it is actually quite stable. It is formaldehyde solution prepared in-house (from paraformaldehyde) that is unstable. So the thing to remember is that if you prepare your own formaldehyde solution, it will not remain at the initial concentration for long, and so you need to use it quickly.

Yes. I did prepare my own formaldehyde from the vial that we purchased. The commercially available one was 16% methanol free and I diluted it to 4% in PBS. ON reading your answers, I doubt whether its this step that has gone wrong so that Iam not able to get the required result. Thank you guys. 

Personally I’m getting crazy with continues error repetition by the scientific community in their articles. They commonly stand fixation with 4% PFA, while it is a powder/polymer forme of formaldehyde, having no fixative properties. Sometimes I want to ask them if they spreaded the PFA powder over the tissue and waited for a miracle fixing… We are scientists and we should use the correct nomenclature.

I think saying that you use 4%PFA generally implies it has been put into solution, which requires the heating, etc which give it fixative properties. You are correct but kind of a moot point.

Kyle, the correct abbreviation of formaldehyde is FA and PFA stands for paraformaldehyde. The problem is that people repeat continuesly this error that it bekame a standard use. It doesn’t change a fact that it’s an error. If someone would like to stand for a bufferred solution of formaldehyde, no problrm use a correct way, e.g., PBS-FA.

I stand corrected and will do my best to use PBS-FA in my methods of upcoming papers. Thanks!

https://cellculture2.altervista.org/protocol-4-paraformaldehyde-solution-in-pbs/

Paraformaldehyde is a chemicdl name polyoxymethylene in the powder form of polymerized formaldehyde that by itself cannot fix the tissues and to be usable as a tissue fixative .paraformaldehyde has to be dissolved in hot water or pbs to become a formaldehyde solution.

Dear colleagues,

I have question and I need some help if you are availabe.

We need to transport rat tissues in phosphate bufered 4% paraformaldehyde (as recommended).However, we don’t have paraformaldehyde - we only have PBS and formaldehyde 38-40% w/v - is IT possible to use this solution of formaldehyde. If it is, gow could I prepare IT?

thank you for your time

kind regards