To examine whether diffusion-weighted magnetic resonance imaging (DWI) is as useful as fluorodeoxyglucose positron emission tomography (FDG-PET) for discriminating between malignant and benign pulmonary nodules measuring less than 3 cm in size, as well as for predicting tumor aggressiveness. PET and DWI were carried out on 87 pulmonary nodules measuring from 1 to 3 cm in size (66 NSCLCs and 21 benign nodules). The signal intensity (SI) of DWI was measured by the contrast ratio (CR) between the lesions and spinal cord, i.e., SI-CR. The maximum standard uptake value (SUV) of PET was measured by CR between the lesions and contralateral lung, i.e., SUV-CR. DWI and PET showed sensitivities of 0.86 and 0.71, and specificities of 0.90 and 0.81, respectively. While there was no significant difference in the specificity between the two, DWI showed a significantly higher sensitivity than PET (p = 0.013). While the difference in the sensitivity was significant in lung adenocarcinoma (p = 0.012), there was no difference in the other histological types. Both the SI-CR and SUV-CR were significantly higher in the tumors with either histological invasiveness or lymphatic metastasis than in those without. DWI is thus considered to be useful, not only to diagnose NSCLCs, especially in lung adenocarcinoma, but also for predicting tumor aggressiveness as well as FDG-PET.