This study aimed to document the effects of an eight hour journey on behavioural, clinical, haematological, environmental and respiratory parameters, and to identify possible associations between factors. Twelve horses underwent clinical examination, respiratory endoscopy with tracheal wash (TW) aspiration, and collection of venous and arterial blood before (BJ) and after the journey (AJ). TW were submitted for conventional quantitative bacteriological evaluation and genetic microbiome analyses. Behaviour was assessed in stables prior to transportation and throughout the journey. Transportation caused mild, but significant, effects on fluid and electrolyte balance and an acute phase response, characterized by neutrophilia, hyperfibrinogenaemia and hyperglobulinaemia. The proportion of neutrophils in TW, tracheal mucus and TW bacterial concentration was increased AJ, with preferential replication of Pasteurellaceae. Horse behaviour en route predicted clinical and respiratory outcomes. The frequency of stress related behaviours was greatest in the first hour of the journey, and balance-related behaviours were most common in the final hour of the journey. Horses which lowered their heads less frequently en route and showed more stress-related behaviours had higher physiological stress (serum cortisol and heart rate on arrival), increased tracheal mucus and inflammation scores, and higher TW bacterial concentration AJ (P<0.05). Six horses with abnormal lung auscultation AJ proved to have had higher tracheal inflammation scores at preloading (P = 0.017), an overall higher concentration of bacteria in their TW (P = 0.013), and an increased percentage of neutrophils in TW at five days AJ (P = 0.003) in comparison to the other horses. While transport-related health problems are multifactorial, clinical examination, including auscultation and endoscopic inspection of the lower respiratory tract before and after journey, and behavioural observation en route may identify animals at increased risk of transport associated respiratory disease.