Purpose of Review: In this review, we summarize updates in the diagnostic approach of headaches with the aim of facilitating the distinction between primary and secondary etiology in headaches. Recent Findings: In the USA, headache is the fifth most common complaint in the emergency department, but only a minority will have a secondary etiology. Initial suspicion and diagnostic workup of secondary headache relies on a patient’s medical history due to a scarcity of validated biomarkers. A special interest group under the International Headache Society recently synthesized information on red flags (information that indicates a secondary etiology) and green flags (information that indicates a primary etiology). A systematic diagnostic approach using red flags and green flags can help reduce unnecessary testing and shift attention to patient care. Summary: Going forward, further validation of these concepts is needed to properly introduce them for clinical use.