The effect of photodynamic therapy treatments depends on the concentration of photosensitizer at the treatment site; thus a simple method to quantify concentration is desirable. This study compares the concentration of a fluorophore and sensitizer, aluminum phthalocyanine tetrasulfonate (AlPcS4), measured by two simple fluorescence-based techniques in vivo to post mortem chemical extraction and fluorometric assay of those tissues: skin, muscle, fascia, liver, and kidney (cortex and medulla). Fluorescence was excited and detected by a single optical fiber, or by an instrument that measured the ratio of the fluorescence and excitation reflectance. The in vivo measurements were compared to calibration measurements made in tissue-simulating phantoms to estimate the tissue concentrations. Reasonable agreement was observed between the concentration estimates of the two instruments in the lighter colored tissues (skin, muscle, and fascia). The in vivo measurements also agreed with the chemical extractions at low (<0.6 µg/g) tissue concentrations, but underestimated higher tissue concentrations. Measurements of fluorescence lifetime in vivo demonstrated that AlPcS4 retains its mono-exponential decay in skin, muscle, and fascia tissues with a lifetime similar to that measured in aqueous tissue-simulating phantoms. In liver and kidney an additional short lifetime component was evident.