Background There is emerging evidence that the supplementation of omega-3 contributes to a decrease in aggressive behaviour in prison populations. A challenge of such research is achieving statistical power against effect sizes which may be affected by the baseline omega-3 index. There are no published data on the blood omega-3 index with studies of this kind to assess the variability of the blood omega-3 index in conjunction with aggression and attention deficit assessments. Objective To determine if the variance of the omega-3 index is correlated with aggressive and attention deficit behaviour in a prison population. Design 136 adult male prisoners were recruited from South Coast Correctional Centre (SCCC), NSW Australia. A 7 point categorisation was used to quantify levels of aggressive behaviour (4 weeks) from individual SCCC case notes, whereby higher scores correspond to increasingly aggressive behaviour. Study participants completed the Aggression Questionnaire (AQ) and the Brown's Attention Deficit Disorder Scales (BADDS), provided a blood sample for erythrocyte fatty acid analysis using gas chromatography and the omega-3 index was calculated. Results The baseline omega-3 index ranged from 2.3% to 10.3%, indicating that some participants already had substantial omega-3 intake, however a median of 4.7% indicated a lower overall omega-3 intake than the general Australian population. Assessment of aggressive and attention deficit behaviour shows that there were negative correlations between baseline omega-3 index and baseline aggression categorisation scores (r = −0.21, P = 0.016); total AQ score (r = −0.234, P = 0.011); Anger (r = -0.222 p = 0.016); Hostility AQ (r = −0.239, P = 0.009); indirect aggression (r = −0.188 p = 0.042); total BADDS (r = −0.263, p = 0.005); Activation (r = −0.224, p = 0.016); Attention (r = −0.192, p = 0.043); Effort (r = −0.253, p = 0.007); Affect (r = −0.330, p = 0.000) and Memory (r = −0.240, p = 0.010). Conclusions There is a high variability in omega-3 status of a NSW prison population, and inmates with lower omega-3 index were more aggressive and had higher ADD scores.