Treatment with protease inhibitors results in a dose-dependent accumulation of the GFP, which can be used to calculate the drug IC50. In the present study, we extended, improved and validated with clinical samples this phenotypic assay. We modified the cloning vector to facilitate the introduction of HIV-1 proteases from HIV-1 isolates of infected subjects. To do so, we replaced the original HIV-1 protease from the plasmid containing the GFP–PR with a polylinker before cloning 46 clinical isolates to further evaluate the method. We also improved detection of the GFP reporter gene using the molecular mechanism described above. When comparisons between values obtained by our assay and those of classic phenotyping assays were performed, the results showed that our method had a high degree of reliability and was comparable to other, widely used assays based on both genotypic and phenotypic data. Excellent correlations coefficients were observed in all cases. Therefore, we were able to evaluate and validate the predictive potential of our noninfectious method.