Background: Most accounts of deployment mental health in UK armed forces personnel rely on retrospective assessments. Aims: We present data relating to the burden of mental ill health and the effect of support measures including operational, family, welfare and medical support obtained on two occasions some 18 months apart. Method: A total of 2794 personnel completed a survey while deployed to Afghanistan; 1363 in 2011 and 1431 in 2010. Their responses were compared and contrasted. Results: The prevalence of self-report mental health disorder was low and not significantly different between the surveys; the rates of probable post-traumatic stress disorder (PTSD) were 2.8% in 2010 and 1.8% in 2011; for common mental health disorders the rates were 17.0% and 16.0% respectively. Remembering receiving predeployment psychoeducation, perceptions of good leadership and good family support were all significantly associated with better mental health. Seeking support from non-medical sources and reporting sick for medical reasons were both significantly associated with poorer mental health. Conclusions: Over a period of 18 months, deployment mental health symptoms in UK armed forces personnel were fewer than those obtained from a military population sample despite continuing deployment in a high-threat context and were associated with perceptions of support.