Aggregation and membrane penetration of porphyrinic photosensitizers play crucial roles for their efficacy in photodynamic therapy. The current study was aimed at comparing the aggregation behavior of selected photosensitizers and correlating it with membrane affinity. Self-assembling properties of 15 amphiphilic free-base chlorin and porphyrin derivatives bearing carboxylate substituents were studied in phosphate buffered saline (PBS) by H-1 NMR spectroscopy, making use of ring current induced aggregation shifts. All compounds exhibited aggregation in PBS to a different degree with dimers or oligomers showing slow aggregate growth over time. Aggregate structures were proposed on the basis of temperature dependent chemical shift changes. All chlorin compounds revealed similar aggregation maps with their hydrophobic sides overlapping and their carboxylate groups protruding toward the exterior. In contrast, for the porphyrin compounds, the carboxylate groups were located in overlapping regions. Membrane interactions were probed using 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer vesicles and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles as models. The chlorin derivatives had higher membrane affinity and were all monomerized by DHPC micelles as opposed to the porphyrin compounds. The observed differences were attributed to the different aggregate structures proposed for the chlorin and porphyrin derivatives. Free accessibility of the carboxylate groups seemed to promote initial surface interaction with phospholipid bilayers and micelles.