I am curious, what do you mean by inner filter? What is the instrument you are using?

The inner filter effect (IFE) is the reduction of fluorescence intensity of a fluorophore that results from absorbance of the excitation or emission light by the fluorophore itself or by another substance.

If the IFE is caused by a high concentration of the fluorophore itself, it will be apparent from the non-linearity of a plot of fluorescence intensity v. fluorophore concentration. However, this could also be caused by self-quenching.

A typical example of the IFE caused by a second compound occurs when measuring the effect of a ligand on the intrinsic tryptophan fluorescence of a protein. The method for measuring the IFE and correcting for it is straightforward. The ligand titration is repeated using N-acetyltryptophanamide (NATA) as a substitute for the protein. The wavelength settings are unchanged. Since the ligand doesn't bind to NATA (presumably), any reduction in NATA fluorescence is attributable to the IFE. The IFE correction factor multiplier to be applied to the titration of the protein is the ratio of the NATA fluorescence without the ligand to the NATA fluorescence with the ligand at each concentration.

This approach can be done in a single-cuvette fluorometer, using separate titrations.

Is this to say that inner filter is in fact dichroic filter cutting off unwanted frequencies? Are you using grating based fluorometer or filter based? I am sorry that this discussion is not completely in the line of answering your question at the moment, but I just need to understand this completely.

Nebosja, The inner filter effect is confusingly named, since it has nothing to do with the optical filters used in some fluorimeters. It is a phenomenon of the sample, not the instrument. It is really just absorbance.

Adam, thank you for insight. Apparently I am not familiar with this field use of fluorescence, in some other fields yes, of course. I use it often. However, upon your answer I have googled this application field and it seems to me (as an ignorant really in the matter)  that some useful info might be readily available at http://www.mrc-lmb.cam.ac.uk/rlw/text/tutorials/inner_filter_correction.htm . I could be wrong of course, since this could be well know info, but anything that may help is worth of checking. Thank you once again.

If the sample fluorescence intensity is high enough to allow you to sacrifice some of it, you can reduce the inner filter effect by using a shorter path length. This means using a thinner cuvette. Instead of a 1 x 1 cm cuvette, you could use a 0.4 x 0.4 cm cuvette, for example. If the IFE predominantly affects only excitation OR emission but not both, you could use a 0.2 x 1 cm cuvette.. By reducing the size of the IFE, you need smaller correction factors.