To our knowledge, studies concerning the prevalence and burden of primary headache in China are limited to specific regions without comparison of different districts. A survey in a different area with similar climate and culture may enhance our knowledge of the factors causing primary headache and the burden of headache. We conducted a 1 year survey on the prevalence and burden of primary headache in the Chinese provinces of Guangdong and Guangxi. Our study also evaluated the factors behind similarities and differences affecting prevalence in the two regions of study. The survey methodology, which was used in an Expanded Program on Immunization by the World Health Organization, was adopted to investigate the prevalence and burden of headache patients. Random samples of 372 local residents in Guangdong and 182 local residents in Guangxi aged 18-65 years were invited to a face-to-face interview. The education level and mean household income were higher in Guangdong (p<0.05). The 1 year prevalence of primary headache was 22.6% (84/372) in Guangdong and 41.2% (75/182) in Guangxi (p<0.001). The average financial burden of primary headache is 2.1% and 3.7% of the mean household income in Guangdong and Guangxi, respectively (p=0.001). The district with lower economic status had a higher prevalence of primary headache, and inevitably bears a heavier burden even with the same disease cost. Copyright © 2014. Published by Elsevier Ltd.