We prospectively assessed inter-observer agreement in the diagnosis of recurrent headaches in children. Clinical letters containing information on 40 children with headaches (age 4.3 to 17.8 years, median 10.4 years) were given to four Pediatric Neurologists. One or more headache types could be checked off on a data sheet that listed the main types recognized by the International Headache Society and an additional one, “combined migraine and tension-type headache”. There were six combinational pairs of neurologists. The six pairs yielded 240 sets of diagnoses. Percentage agreement ranged from 45% to 78%, Kappa values from 0.20 to 0.59, and weighted Kappa from 0.19 to 0.52 within the six pairs. Agreement was 76% when both neurologists in a pair assigned single headache types and 4% when one or both neurologists diagnosed multiple types. The International Headache Society suggests that patients may have multiple types of headache and recommends that all types be classified. We suggest that the option of diagnosing more than one headache type from data in clinical letters may reduce inter-observer agreement.