One person went to the dentist's. The dentist pulled out a tooth, so the patient screamed. Because of that two other patients left the dentist's. The patient got the bill. The bill was so high. He called the dentist and said 'It is too expensive.'.......

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What does 'it' refer to in the last sentence? I know when the subject is 'the bill', we use high or low. Right? When we use expensive, the subject should be .....(what)?

First of all, I'd just say, "... to the dentist." (Or maybe "to the dentist's office.")

In the last sentence, "it" seems to refer to the cost of the procedure the dentist was performing. (Tooth extraction.)

If "it" is too vague (and I think it is since there's no clear antecedent for it), then the word "procedure" can be the subject.

And, yes, when referring to "the bill," you use "high" or "low."

In the last sentence, 'it' refers to the bill. You are correct that when referring to the cost of something, we typically use high or low. However, 'expensive' can also be used to describe the bill because it is an adjective that means something is costing a lot of money. In this case, the subject of the sentence is the bill, and 'it' is a pronoun that refers back to the bill.