Strangely enough, that's a difficult question to answer. Part of the problem is that scientific words can be made very long indeed, but such words are not used in conversation; they are simply descriptions, usually of complex organic chemicals, and are simply made by stringing lots of chemical names together.
A common answer to this question is "antidisestablishmentarianism" (28 letters) which means "opposition of those who oppose the link between Church and State". The Guinness Book of Records lists "floccinaucinihilipilification" (29 letters), which means "the estimation of a thing as worthless".
The word "pneumonoultramicroscopicsiliocovolcanoconiosi s" (46 letters) is supposed to refer to a disease caused by the inhalation of dust, but in fact this word is a hoax -- it's not a real word at all.
In science, though, words can be as long as you like. The full chemical description of a protein called "titin" is 189,819 letters long. In case you're interested, titin consists of 132,983 atoms of carbon, 211,861 of hydrogen, 36,149 of nitrogen, 40,883 of oxygen and 693 of sulphur.
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