The interactions of three cationic distyryl dyes, namely 2,4-bis(4-dimethylaminostyryl)-1-methylpyridinium (1 a), its derivative with a quaternary aminoalkyl chain (1 b), and the symmetric 2,6-bis(4-dimethylaminostyryl)-1-methylpyridinium (2 a), with several quadruplex and duplex nucleic acids were studied with the aim to establish the influence of the geometry of the dyes on their DNA-binding and DNA-probing properties. The results from spectrofluorimetric titrations and thermal denaturation experiments provide evidence that asymmetric (2,4-disubstituted) dyes 1 a and 1 b bind to quadruplex DNA structures with a near-micromolar affinity and a fair selectivity with respect to double-stranded (ds) DNA [Ka(G4)/Ka(ds)=2.5–8.4]. At the same time, the fluorescence of both dyes is selectively increased in the presence of quadruplex DNAs (more than 80–100-fold in the case of human telomeric quadruplex), even in the presence of an excess of competing double-stranded DNA. This optical selectivity allows these dyes to be used as quadruplex-DNA-selective probes in solution and stains in polyacrylamide gels. In contrast, the symmetric analogue 2 a displays a strong binding preference for double-stranded DNA [Ka(ds)/Ka(G4)=40–100), presumably due to binding in the minor groove. In addition, 2 a is not able to discriminate between quadruplex and duplex DNA, as its fluorescence is increased equally well (20–50-fold) in the presence of both structures. This study emphasizes and rationalizes the strong impact of subtle structural variations on both DNA-recognition properties and fluorimetric response of organic dyes.