Polymers when self-cross-linked into single-chain nanoparticles bear some resemblance to folded proteins; yet proteins have clear energy landscapes that determine precisely folded structures, while single-chain polymer nanoparticles (SCNPs) have more undefined structures. There have been initial reports showing that some structural parameters in SCNPs can be controlled, for example, compactness. Here, we construct SCNPs from poly(allylamine) (M-w similar to 22 000 Da) with dicarboxylic acids (HOOC-R-COOH) in solvent conditions, where initial chains adopt either extended or collapsed conformation. The spacer groups R that we used were -CH2CH2-, -(CH2S)(2)-, or -(CH2CH2)(3)-, whose length can be estimated to vary from similar to 4 to similar to 12 A. We present a systematic study that uses several characterization techniques (H-1 NMR diffusion-ordered spectroscopy (DOSY), viscometry, analytical ultracentrifugation, and H-1 NMR T-2 relaxation) to show that both initial reaction conditions as well as length of cross-linking molecules determine the final compactness of SCNPs. Specifically, when short cross-linking molecules are applied, short-range loops dominate and the cross-linking process fails to achieve global chain compaction, leading to less compact SCNPs. When the chain is precollapsed (0.1 M water solution of NaCl or 10 vol % ethanol as opposed to DI water), the particles resulting after cross-linking are more compact. Of utmost practical relevance, we show that particles that are essentially chemically identical but differ only in compactness have different toxicity when interacting with HeLa cells, the more compact ones being less toxic.