The misfolding of a soluble proteins into insoluble aggregates is a common underlying event in a number of human diseases such as Alzheimer's disease, Polyglutamine disorders, Type II diabetes etc. Understanding the molecular mechanisms that initiate and drive the process is important for protein folding and design studies. In addition to the biophysical studies, in vivo screens that provide an unbiased and model-free approach are required in order to elucidate sequence-aggregation relationship. These screens allow for a rapid analysis of a number of sequences and can also be utilized to select potential aggregation inhibitors. In the present study we focused on two separate screens to assess aggregation propensities of a suite of test proteins. The test proteins are fused upstream to a reporter protein and the result of the screen is a function of folding of the entire fusion construct. A set of proteins that are known to form fibers in vitro, were fused to two reporter proteins: Green Fluorescent Protein (GFP) and Chloramphenicol Acetyltransferase (CAT). The misfolding of the test protein upstream results in fluorescence inhibition in GFP, and a decrease in enzyme activity for CAT. Based on our findings we conclude that the utility of the GFP assay is that of a rapid screen while the CAT assay can be utilized for explicit selection. We also discovered that the CAT assay was more effective in elucidating the subtle differences in protein misfolding than GFP assay.