Titania-supported palladium, gold and bimetallic nanoparticles (second-generation nanoparticles) demonstrate promising photocatalytic properties. However, due to unusual reactivity, second-generation nanoparticles can be hazardous for living organisms. Considering the ever-growing number of new types of nanoparticles that can potentially contaminate the environment, a determination of their toxicity is extremely important. The main aim of presented study was to investigate the cytotoxic effect of surface modified TiO₂-based nanoparticles, to model their quantitative nanostructure–toxicity relationships and to reveal the toxicity mechanism. In this context, toxicity tests for surface-modified TiO₂-based nanoparticles were performed in vitro, using Gram-negative bacteria Escherichia coli and Chinese hamster ovary (CHO-K1) cells. The obtained cytotoxicity data were analyzed by means of computational methods (quantitative structure–activity relationships, QSAR approach). Based on a combined experimental and computational approach, predictive models were developed, and relationships between cytotoxicity, size, and specific surface area (Brunauer–Emmett–Teller surface, BET) of nanoparticles were discussed.