Our objective was to evaluate whether thrombocytopenia and small thymus volume, which may be associated with hazardous alcohol consumption, are predictors of cognitive performance after highly-active antiretroviral treatment (HAART). To achieve this goal 165 people living with HIV starting HAART underwent thymus magnetic resonance imaging, cognitive (HIV Dementia Score [HDS] and the California Verbal Learning Test [CVLT]), immune and laboratory assessments at baseline and after 6 months of HAART. At baseline, hazardous alcohol consumption was significantly correlated with both thymus size (r = -0.44, p = 0.003) and thrombocytopenia (r = 0.28, p = 0.001). Of interest, thrombocytopenic patients were characterized by a smaller thymus size. Individuals with and without cognitive impairment differed in alcohol consumption, platelet counts and thymus size, suggesting that they may be risk factors for neurological abnormalities. In fact, after HAART hazardous alcohol use associations with thrombocytopenia were related to cognitive decline (learning = -0.2 +/- 0.8, recall = -0.3 +/- 0.1 and HDS = -0.5). This contrasted with improvements on every cognitive measure (learning = 1.6 +/- 0.3, p = 0.0001, recall = 2.2 +/- 0.4, p = 0.0001 and HDS = 1.0, p = 0.05) in those with neither alcohol use nor thrombocytopenia. In adjusted analyses for sociodemographics, adherence and immune measurements, reduced thymus size was associated with a 90% and thrombocytopenia with a 70% increase in the risk of scoring in the demented range after HAART (RR = 1.9, p < 0.05 and RR = 1.7, p = 0.03) and with low CVLT scores (thymus volume RR = 2.0, p = 0.04, chronic alcohol use p = 0.05 and thrombocytopenia p = 0.06). Thymus volume and platelet counts were negatively affected by alcohol and were predictors of cognitive performance and improvements after HAART. These results could have important clinical and therapeutic implications.