We present an update of the LXTX correlation using a large data sample of 180 GRBs with well sampled light-curves. Since this correlation can partially result from the redshift dependences of these intrinsic parameters (namely their cosmological evolution), we use the Efron-Petrosian method to reveal the intrinsic nature of this correlation. We show that a substantial part of the correlation is intrinsic. We describe how we recover it and how it can be used to constrain physical models of the plateau emission, whose origin is still unknown. We then extend the analysis of the LXTX relation to study correlations between the afterglow and prompt emission. We find a tight physical scaling between the afterglow luminosity Lx and the mean luminosities of the prompt emission. The most highly correlated subsample in the afterglow leads also to the most clear prompt–afterglow correlation. Such events can be considered the "standard GRBs" for cosmological applications. Finally, we investigate how changes of the observed slopes, bobs, of the LXTX correlation in GRB afterglows can affect the determination of cosmological parameters. Using 101 simulated GRBs with a central value of bobs that differs from the intrinsic one by 5σ, we find an overestimated value of the matter density parameter ΩM compared to that obtained from Ia SNe; while for the Hubble constant H0, our best fit value is still compatible at 1σ level. Instead, using a subsample of highly luminous GRBs (‘HighL'), H0 and ΩM are no longer compatible at 1σ and ΩM is underestimated by 13%. However, the HighL sample dramatically reduces the intrinsic scatter of the correlation, thus possibly identifying this sample as the standard ‘canonical' GRBs. We conclude that any approach to cosmology should take into consideration only the intrinsic correlations, not the observed ones.