AMPKalpha is a subunit of AMP-activated protein kinase (AMPK), a heterotrimeric enzyme that works as a fuel sensor activated in response to the depletion of cellular ATP. AMPKalpha is considered as a master switch in regulating glucose and lipid metabolism. Determining its presence in patient sera may help in diagnosing metabolic diseases. Using isoelectric focusing and Western blotting, we were able to detect AMPKalpha in human sera. Using specific antibodies, we showed that the AMPKalpha1 and alpha2 isoforms were apparently present in equal amounts in human sera. To characterize normal and abnormal AMPKalpha patterns, we used an antibody which recognized both isoforms (alpha1 and alpha2) to analyze sera of patients and healthy individuals. We also analyzed sera of HIV patients because several studies suggest that AMPK may play a role in the mechanism of lipodystrophy in HIV patients under antiretroviral therapy. We found that patients with type 2 diabetes or liver diseases presented abnormal AMPK IEF patterns. AMPK was poorly detectable in sera of patients with end-stage liver disease. Abnormal AMPK IEF patterns were more frequent in treated HIV-patients compared to those who are untreated suggesting a possible association between AMPK and the side-effects of antivirals. Our findings highlight the potential of serum AMPK as a new diagnostic biomarker and may help to study the regulation of AMPK activity in tissues.