Whole organs or sections of organs are removed during surgical surgeries and are larger specimens. A uterus after a hysterectomy, the big bowel after a colectomy, or the tonsils after a tonsillectomy is all examples. Biopsies are minor surgical procedures that remove pieces of the tissue rather than full organs. They are generally conducted while the patient is awake but sedated. Excision biopsies, in which tissue is removed using a scalpel, and core biopsies, in which a needle is put into a suspicious mass to extract a sliver of tissue that can be viewed under a microscope, are two types of biopsies.

A fine-needle aspiration can be used to extract fluid and very minute fragments of tissue (FNA). This procedure is done with a thinner needle than a core biopsy, but the methodology is the same. This sort of sample is usually liquid rather than solid, and it is sent to cytology rather than histology for analysis.

Specimens received by the pathology laboratory must first be prepared for analysis, after which they are processed and analyzed using techniques suited for the kind of tissue and the inquiry needed.

A frozen section is used for quick diagnosis during a surgical procedure, which may alter the sort of surgery conducted.