BackgroundHigh-altitude headache (HAH) is the most common sickness occurred in healthy people after rapid ascending to high altitude, and its risk factors were still not well understood. To investigate physiological, hematological and biochemical risk factors associated with high-altitude headache (HAH) after acute exposure to 3700 m, we conducted a two-stage, perspective observational study. In 72 h, total 318 young Han Chinese males ascended from sea level (altitude of 50 m) to altitude of 3700 m by train. Demographic data, physiological, hematological and biochemical parameters of all participants were collected within one week prior to the departure, and within 24 h after arrival.ResultsThe incidence of HAH was 74.84%. For parameters measured at sea level, participants with HAH exhibited significantly higher age and lower BUN (p < 0.05). For parameters measured at 3700 m, participants with HAH exhibited significantly lower blood oxygen saturation (SpO2), higher resting heart rate (HR), higher systolic blood pressure at resting (SBP) and lower blood urea nitrogen (BUN) (all p < 0.05). At 3700 m, the severity of HAH associated with SpO2, HR and BUN significantly (all p < 0.05). Multivariate logistic regression revealed that for parameters at sea level, BUN was associated with HAH [BUN (OR:0.77, 95% CI:0.60–0.99)] and for parameters at 3700 m, SpO2, HR and BUN were associated with HAH independently [SpO2 (OR:0.84, 95% CI:0.76–0.93); HR (OR:1.03, 95% CI:1.00–1.07); BUN (OR:0.64, 95% CI:0.46–0.88)]. No association between hematological parameters and HAH was observed.ConclusionWe confirmed that higher HR, lower SpO2 are independent risk factors for HAH. Furthermore, we found that at both 50 m and 3700 m, lower BUN is a novel independent risk factor for HAH, providing new insights for understanding the pathological mechanisms.Electronic supplementary materialThe online version of this article (10.1186/s10194-018-0878-7) contains supplementary material, which is available to authorized users.