The impact of host factors, such as gender and co-morbidity, on mortality after trauma has been debated. Quantification of risk factors is dependent on methodological considerations including follow-up time, definitions and adjustment of potential confounders. Optimal follow-up time of trauma patients remains to be elucidated. We investigated the impact of gender and co-morbidity on short and long term mortality in a cohort including 4,051 patients from a level 1 trauma centre. Data from the trauma cohort were linked to validated national registries. 30 and 360-day survival were analysed with logistic and Cox regression, respectively. Long term survival was also estimated as standardized mortality ratio, which implies a comparison with a matched general population. The influence of host factors on outcome after trauma differed over time. Male gender was an independent risk factor for mortality at 1 year but not at 30-days post-injury, even after adjustment for clinically relevant confounders. This gender difference was also apparent when comparing mortality rates with the general population. Moreover, the effect of gender seems to be restricted to elderly patients. The presence of co-morbidity became a significant risk factor beyond 30 days after trauma, suggesting that this patient group may benefit from a more thorough follow up after hospital discharge. A persistent excess mortality compared to the general population was still seen 1 year after the trauma. Our findings indicate that the effect of trauma is not limited to the early post-injury period but adversely affects the long term outcome.