The present invention relates to a disease diagnosis method, a marker screening method, and a marker using a time-of-flight secondary ion mass spectrometry (TOF-SIMS), and more particularly, to a large intestine cancer diagnosis method, a large intestine cancer marker screening method, and a large intestine cancer marker using a time-of-flight secondary ion mass spectrometry (TOF-SIMS). Specifically, the present invention provides a method diagnosing a disease using a pattern of secondary ion mass (m/z) peaks of biological samples measured using a time-of- flight secondary ion mass spectrometry (TOF-SIMS) as a marker, a marker screening method being a reference judging an existence or non-existence of a disease, and a marker configured of specific secondary ion mass peaks.