The present study aimed to assess gadoxetate disodium contrast-enhanced (CE) positron emission tomography (PET)/magnetic resonance imaging (MRI) with Ga-68-DOTATOC and C-11-5-Hydroxy-tryptophan (C-11-5-HTP) in comparison with iodine CE Ga-68-DOTATOC-PET/computed tomography (CT) for neuroendocrine tumour imaging. Detection rate and reader's confidence were evaluated for each separate image volume: CE-CT, CE-MRI including diffusion-weighted imaging, Ga-68-DOTATOC-PET performed at PET/CT, Ga-68-DOTATOC-PET performed at PET/MRI and C-11-5-HTP-PET, and for the three combined hybrid examinations Ga-68-DOTATOC-PET/MRI, C-11-5-HTP-PET/MRI and Ga-68-DOTATOC-PET/CT. In 11 patients, 255 lesions were depicted. Ga-68-DOTATOC-PET performed at PET/MRI depicted 72.5%, Ga-68-DOTATOC-PET performed at PET/CT depicted 62.7%, C-11-5-HTP-PET depicted 68.2% and CE-CT depicted 53% of lesions. Ga-68-DOTATOC-PET performed at PET/MRI (P < 0.001) and PET/CT (P = 0.02), C-11-5-HTP-PET (P < 0.001) and MRI (P < 0.001) were superior to CT. Ga-68-DOTATOC-PET/MRI and C-11-5-HTP-PET/MRI detected 92.5% and 92% of lesions, respectively, and both outperformed Ga-68-DOTATOC-PET/CT (65%) (P < 0.001). For liver metastasis imaging, MRI alone was unsurpassed (P < 0.01) and Ga-68-DOTATOC-PET/MRI and C-11-5-HTP-PET/MRI outperformed Ga-68-DOTATOC-PET/CT (P < 0.001). For lymph node metastasis diagnosis, Ga-68-DOTATOC-PET performed at PET/MRI and PET/CT and C-11-5-HTP-PET detected 94%, 94% and 94% of lesions, respectively, and outperformed MRI and CE-CT alone (P < 0.001). For bone metastasis imaging, Ga-68-DOTATOC-PET performed at PET/MRI and PET/CT and C-11-5-HTP-PET performed equally well (P = 0.05) and better than MRI. Reader's confidence was better for Ga-68-DOTATOC-PET/MRI and C-11-5-HTP-PET/MRI than for Ga-68-DOTATOC-PET/CT. The tumour maximum standardised uptake value and tumour-to-liver ratio were both approximately twice as high as for Ga-68-DOTATOC than for C-11-5-HTP. Ga-68-DOTATOC-PET/MRI and C-11-5-HTP-PET/MRI provided the highest detection rates and reader's confidence and were both superior to Ga-68-DOTATOC-PET/CT, mainly because of the MRI component. The imaging contrast with Ga-68-DOTATOC was superior to that of C-11-5-HTP.