AbstractPolyglutamine repeats in proteins are highly correlated with amyloid formation and neurological disease. To better understand the molecular basis of glutamine repeat diseases, structural analysis of polyglutamine peptides as soluble monomers, oligomers, and insoluble amyloid fibrils is necessary. In this study, fluorescence resonance energy transfer (FRET) experiments and molecular dynamics simulations using different theoretical models of polyglutamine were conducted. This study demonstrates that a previously proposed simple CαCβmodel of polyglutamine, denoted as FCO, accurately reproduced the present FRET results and the results of previously published FRET, triplet‐state quenching, and fluorescence correlation studies. Other simple CαCβmodels with random coil and extended β‐strand parameters, and all‐atom models with parm96 and parm99SB force fields, did not match the FRET result well. The FCO is an intrinsically disordered model with a high‐effective persistence length producing extended peptides at short lengths (QN< 10). Because of an increasing number of attractive Q–Q interactions at longer lengths, the FCO model becomes increasingly more compact at lengths between QN∼ 10–16 and is as compact as many folded proteins at QN> 16. Proteins 2011. © 2010 Wiley‐Liss, Inc.