AIMS: Alcohol can induce diverse serious pathologies, yet this complexity may be obscured when alcohol-related deaths are classified according to a single underlying cause. We sought to quantify this issue and its implications for analysing mortality data. DESIGN, SETTING AND PARTICIPANTS: Cross-sectional study included 554 men aged 25-54 in Estonia undergoing forensic autopsy in 2008-09. MEASUREMENTS: Potentially alcohol-related pathologies were identified following macroscopic and histological examination. Alcohol biomarkers levels were determined. For a subset (26%), drinking behaviour was provided by next-of-kin. The Estonian Statistics Office provided underlying cause of death. FINDINGS: Most deaths (75%) showed evidence of potentially alcohol-related pathologies, and 32% had pathologies in two or more organs. The liver was most commonly affected [60.5%, 95% confidence interval (CI) = 56.3-64.6] followed by the lungs (18.6%, 95% CI = 15.4-22.1), stomach (17.5%, 95% CI = 14.4-20.9), pancreas (14.1%, 95% CI = 11.3-17.3), heart (4.9%, 95% CI = 3.2-7.0) and oesophagus (1.4%, 95% CI = 0.6-2.8). Only a minority with liver pathology had a second pathology. The number of pathologies correlated with alcohol biomarkers (phosphatidylethanol, gamma-glytamyl transpeptidase in blood, ethylglucuronide, ethylsulphate in urine). Despite the high prevalence of liver pathology, few deaths had alcoholic liver disease specified as the underlying cause. CONCLUSION: The majority of 554 men aged 25-54 undergoing forensic autopsy in Estonia in 2008-09 showed evidence of alcohol-related pathology. However, the recording of deaths by underlying cause failed to capture the scale and nature of alcohol-induced pathologies found.