Evidence and arguments are summarized that suggest that intrinsic (tryptophan) protein fluorescence provides an excellent and convenient signal for monitoring both GEF (guanine nucleotide exchange factor) and GAP (GTPase activating protein) activity of a large number of small GTPases. In addition, post-translational modifications of Rab proteins occurring in a region known to be a hot spot for such modifications also lead to fluorescence changes that can be accurately monitored in a time-dependent manner. It is suggested that intrinsic fluorescence should be the first method chosen for monitoring such reactions of tryptophan-containing small GTPases. •Intrinsic protein fluorescence - a quick and powerful tool to monitor GEF/GAP activity and post-translational modifications.•Evidence suggests physiological and also pathological importance of post-translational modifications in the switch II region.•Intrinsic fluorescence should be the first method chosen for monitoring such reactions of tryptophan-containing small GTPases.