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Recent studies have suggested that highly active antiretroviral therapy may lead to rises in alanine transaminase (ALT) among HIV-infected patients. However, the definition of an ALT flare is arbitrary and the extent to which such increases represent normal fluctuations has not been explored.Using data from untreated, hepatitis B virus/hepatitis C virus-negative, HIV-infected patients, we derived a definition for an ALT flare by exploring a series of ALT thresholds (from 100 to 200 IU/L). The resulting definition (2 consecutive ALTs > 200 measured >2 weeks apart) was applied to all patients in the UK Collaborative HIV Cohort (CHIC) Study, and Poisson regression was used to identify factors associated with ALT flares.Five hundred and twenty six of 12,206 eligible patients (4.3%) had ≥1 ALT flare, resulting in a total of 615 episodes of ALT flares. The overall rate of an ALT flare was 1.19 (95% confidence interval: 1.10 to 1.28) per 100 person-years. Higher risk of ALT flare was associated with lower CD4 counts, detectable viral loads, being under follow-up in earlier calendar years, prior clinical AIDS, receipt of nevirapine either with didanosine/stavudine or without didanosine/stavudine, receipt of ritonavir, detectable anti-hepatitis C virus, and detectable hepatitis B surface antigen.Associations between known risk factors may be under/over estimated if using single values, that is, 1 ALT > 200, to define ALT flares. We recommend studies to use a more stringent measure and suggest our derived definition of an ALT flare.