When charting on a patient, and a choice is high cholesterol, should both be capitalized?
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Neither word is a proper noun, so technically neither should be capitalized. If you want to capitalize them in "title case" (where terms exist outside of normal syntax and actually form a kind of title), go right ahead and capitalize whatever you want.
If I were filling in a chart, I would certainly capitalize both words, as in "High Cholesterol". In any charting situation, clarity is the chief goal and capitalized words tend to be more easily read or referenced in cramped spaces -- crucial for important words.
Of course, high and cholesterol are not proper nouns and so should not be capitalized within a sentence. Thus, capitalizing them here would certainly be a matter of style. Since you are probably in a medical environment, I would suggest taking a peek at other colleagues' charts to see what the preferred style is. Here is a sample I found.