Submicron-diameter carbon fibers (SCFs) are a type of fine-diameter fibrous carbon material that can be used in various applications. To accelerate their practical application, a hazard assessment of SCFs must be undertaken. This study demonstrated the pulmonary toxicity, cytotoxicity, and genotoxicity of three types of SCFs with different diameters and lengths. The average diameter and length of SCFs were 259.2 nm and 11.7 μm in SCF1 suspensions, 248.5 nm and 6.7 μm in SCF2 suspensions, and 183.0 nm and 13.7 μm in SCF3 suspensions, respectively. The results of pulmonary inflammation and recovery following intratracheal instillation with SCFs at doses of 0.25, 0.5, or 1.0 mg/kg showed that the pulmonary toxicity of SCFs was SCF3 > SCF1 > SCF2. These results suggest that SCF diameter and length are most likely important contributing factors associated with lung SCF clearance, pulmonary inflammation, and recovery. Furthermore, SCFs are less pulmonary toxic than bent multi-walled carbon nanotubes. Cell viability, pro-inflammatory cytokine and intracellular reactive oxygen species productions, morphological changes, gene expression profiling in NR8383 rat alveolar macrophage cells showed that the cytotoxic potency of SCFs is: SCF3 > SCF1 > SCF2. These results showed that SCFs with small diameters had high cytotoxicity, and SCFs with short lengths had low cytotoxicity. We conclude that pulmonary toxicity and cytotoxicity are associated with the diameter and length distributions of SCFs. In addition, a standard battery for genotoxicity testing, namely the Ames test, an in vitro chromosomal aberration test, and a mammalian erythrocyte micronucleus test, demonstrated that the three types of SCFs did not induce genotoxicity. Our findings provide new evidence for evaluating the potential toxicity of not only SCFs used in this study but also various SCFs which differ depending on the manufacturing processes or physicochemical properties.