Sensitive methods have been developed to measure laser-induced fluorescence from trapped ions by reducing the detection of background scattering to zero levels during the laser excitation pulse. The laser beam diameter has been reduced to ϳ150 m to eliminate scattering on trap apertures and the resulting laser-ion interaction is limited to a volume of ϳ10 Ϫ5 cm 3 which is ϳ0.03-0.15 of the total ion cloud volume depending on experimental conditions. The detection optics collected fluorescence only from within the solid angle defined by laser-ion interaction volume. Rhodamine 640 and Alexa Fluor 350 ions, commonly used as fluorescence resonance energy transfer (FRET) fluorophores, were generated in the gas phase by using electrospray ionization and injected into a radiofrequency Paul trap where they were stored and exposed to Nd:YAG laser pulses at 532 and 355 nm for times up to 10 m. Fluorescence emitted by these ions was investigated for several trap q z values and ion cloud temperatures. Analysis of photon statistics indicated an average of ϳ10 photons were incident on the PMT detector per 15 ns pulse for ϳ10 3 trapped ions in the interaction volume. Fluorescence measurements displayed a dependence on trapped ion number which were consistent with calculations of the space charge limited ion density. To investigate the quantitative capability of these fluorescence techniques, the laser-induced fragmentation of trapped Alexa I on traps provide a controlled environment in which fluorescence measurements can be performed on an ensemble of ions over timescales sufficient to consider small ion numbers and slow reaction rates. Laserinduced fluorescence measurements of trapped ions have been used in spectroscopic studies of atomic structure [1][2][3][4], the vibrational spectra of small molecules [5][6][7][8], as well as to characterize the dynamic cooling [9] and crystallization of atomic ions [10 -12].This paper introduces techniques that eliminate the detection of laser background scattering on trap apertures and internal surfaces allowing measurements to achieve both high sensitivity and large dynamic range. In previous pulsed laser measurements of molecular fluorescence collected from trapped species (discussed in references [5][6][7][8]), the radiative lifetimes were sufficiently long to allow collection of fluorescence radiation after the laser pulse. This greatly simplified methods to reduce the detection of background resulting from scattered laser radiation. However, experiments described in this paper apply the Nd:YAG pulsed laser to excite strongly emitting molecules having fluorescence lifetimes shorter than the laser pulse. This required the reduction of background laser scattering during laser excitation, a more demanding constraint.Techniques described in this paper will help to extend fluorescence measurements as an in situ probe of trapped ion properties including chemical identity, the growth and decay of specific ion populations, ion spectroscopy. Fluorescence emission from trapped ions also presen...