Chronic rhinosinusitis (CRS) and primary headache syndromes are common disease entities and headache and facial pain are common reasons for referral to otolaryngology units. Because of an association of nasal symptoms with primary headache syndromes and considerable similarities in their clinical presentations, primary headache syndromes may be misdiagnosed as sinus disease and vice versa. In this review we examine the evidence on which otolaryngologists can base clinical diagnosis and management and offer an approach to distinguishing these common clinical entities.