Single-walled carbon nanotubes (SWNTs) are promising candidates for a wide range of biomedical applications due to their fascinating properties. However, safety concerns are raised on their potential human toxicity and on the techniques that need to be used to assess such toxicity. Here, we integrate for the first time 3D tissue-mimetic models in the cytotoxicity assessment of purified (p-) and oxidized (o-) SWNTs. An established ultrasound standing wave trap was used to generate the 3D cell aggregates, and results were compared with traditional 2D cell culture models. Protein-based (bovine serum albumin) and surfactant-based (Pluronic F68) nanotube dispersions were tested and compared to a reference suspension in dimethyl sulfoxide. Our results indicated that p- and o-SWNTs were not toxic in the 3D cellular model following a 24 h exposure. In contrast, 2D cell cultures were significantly affected by exposure to p- and o-SWNTs after 24 h, as assessed by high-content screening and analysis (HCSA). Finally, cytokine (IL-6 and TNF-R) secretion levels were elevated in the 2D but remained essentially unchanged in the 3D cell models. Our results strongly indicate that 3D cell aggregates can be used as alternative in vitro models providing guidance on nanomaterial toxicity in a tissue-mimetic manner, thus offering future cost-effective solutions for toxicity screening assays under the experimental conditions more closely related to the physiological scenario in 3D tissue microenvironments.