Acute mountain sickness (AMS) is common at high altitude (HA) and associated with a relative failure of the natriuresis and diuresis that occurs at HA. The role of Brain Natriuretic Peptide (BNP) in this context has not been thoroughly investigated. We aimed to clarify if BNP rises in response to exercise at HA and if so whether this is related to AMS. 32 healthy subjects had assessments of BNP, aldosterone and AMS scores [as assessed by the AMS-C score of the Environmental Symptom Questionnaire (ESQ) and Lake Louise questionnaire] made following exertion at sea-level (SL), 3,400, 4,300 and 5,150 m. Data were analysed in the 23 subjects who did not consume drugs known to affect acclimatization. BNP (pg/ml, mean ± SEM) was significantly higher at 5,150 m versus the lower altitudes (p < 0.001 for all): 7.1 ± 1; 6.1 ± 0.3; 6.8 ± 0.9 and 17.7 ± 5.1 at sea-level; 3,400, 4,300 and 5,150 m. In those that showed a BNP response at 5,150 m (n = 19) versus those that did not demonstrate a BNP response (n = 4) there was a significant difference in Lake Louise (LL) AMS scores at 5,150 m on day 10 of the expedition (mean LL score 3.3 vs. 0.75, p = 0.034) and day 11 (mean LL score 3.3 vs. 0, p = 0.003). This is the first report to demonstrate a significant rise in BNP at HA. A BNP response at 5,150 m may be associated with a greater likelihood of suffering AMS.