In the course of a project to identify plant natural products which modulate the susceptibility of different strains of fast-growing mycobacteria to the first-line antituberculotic isoniazid (INH), several flavonoids without significant antimycobacterial activities at the tested concentrations were screened for their ability to decrease the minimum inhibitory concentrations (MICs) of INH. Flavonoids with different substitution patterns, namely epicatechin, isorhamnetin, kaempferol, luteolin, myricetin, quercetin, rutin and taxifolin were tested to examine structure–activity relationships (SARs) of these compounds. Different mycobacterial strains, i.e. Mycobacterium smegmatis (ATCC 14468), M. smegmatis mc2155 (ATCC 700084), M. smegmatis mc22700, M. phlei (ATCC 11758) and M. fortuitum (ATCC 6841) were used. The strongest synergistic effects were observed in M. smegmatis mc2155 followed by M. phlei, whereas the tendency of INH potentiation by certain flavonoids remained the same within each strain. Myricetin was the most efficient intensifier of INH susceptibility in all tested strains causing a decrease of the MIC of INH up to 64-fold at 16 μg/ml, followed by quercetin. Structure–activity relationships of flavonoids as intensifiers of INH susceptibility in mycobacteria indicate that they overlap with SARs for their radical-scavenging properties, however the potentiation of INH activity cannot only be explained by their radical-scavenging activity alone.