Antimicrobial activity of secondary and tertiary poly(diallylammonium) salts (PDAAs) had not been reported before. Due to difficulties with preparation of polymers from the monomers of the diallylamine (DAA) series in the nonquaternary form, up to recently it was not possible to obtain PDAAs with a sufficiently high molecular mass. Here, we describe the investigations of antimicrobial activity of novel water-soluble cationic polyelectrolytes of the PDAA series, namely secondary poly(diallylammonium trifluoroacetate) (PDAATFA) and tertiary poly(diallylmethylammonium trifluoroacetate) (PDAMATFA), in synthesis of which we have recently succeeded, against gram-positive and gram-negative bacteria, and fungi. We have studied the effect of molecular weight (polymeric chain length) and ionic strength of solution on the biocidal efficiency of those polymers; in addition, the concentration dependences of PDAATFA reduced viscosity in salt-free and KCl aqueous solutions have been investigated. The antimicrobial properties of polybase polydiallylamine (BPDAA), which was obtained in an aqueous solution of PDAATFA in presence of alkali, have been also studied as well as biocidal activity of commercial open-chain polybase branched PEI. Those PDAATFA, BPDAA and PEI polymers, served as the systems to study the structure-activity relationships. Transmission electronic microscopy Study was carried out to characterize the mode of antimicrobial action of PDAATFA using E. coli. It was shown that the synthesized PDAATFA and PDAMATFA exhibit, unlike the quaternary polymers of this series, a rather high biocidal efficiency that is comparable with the activity of known effective cationic polymer biocides or exceeds it. Novel polyelectrolytes exhibit quite strong biocidal properties at different conditions including aqueous solutions of moderate ionic strength (serum, 0.01 M/0.1 M) and aqueous-alkaline solutions (pH 10.5) until the macrochain retains some positive charge, but complete neutralization of the polyelectrolyte in a I M salt solution results in the loss of its biocidal activity. The obtained results evidence that the structure of links, which combine the hydrophobic pyrrolidinium rings with the hydrophilic secondary/tertiary ammonium groups, is responsible for the high biocidal activity of the PDAAs. Polymeric nature of the synthesized compounds is one of the most significant factors of their bactericidal efficiency, unlike their high fungicidal activity, which is evidently related to the secondary/tertiary pyrrolidinium cycle.