Purpose Dopamine transporter (DAT) imaging can demonstrate presynaptic dopaminergic neuronal loss in Parkinson's disease (PD). However, differentiating atypical parkinsonism (APD) from PD is often difficult. We investigated the usefulness of dual-phase F-18 FP-CIT positron emission tomography (PET) imaging in the differential diagnosis of parkinsonism. Methods Ninety-eight subjects [five normal, seven druginduced parkinsonism (DIP), five essential tremor (ET), 24 PD, 20 multiple system atrophy-parkinson type (MSA-P), 13 multiple system atrophy-cerebellar type (MSA-C), 13 progressive supranuclear palsy (PSP), and 11 dementia with Lewy bodies (DLB)] underwent F-18 FP-CIT PET. PET images were acquired at 5 min (early phase) and 3 h (late phase) after F-18 FP-CIT administration (185 MBq). Regional uptake pattern of cerebral and cerebellar hemispheres was assessed on early phase images and striatal DAT binding pattern was assessed on late phase images, using visual, quantitative, and statistical parametric mapping (SPM) analyses. Results Striatal DAT binding was normal in normal, ET, DIP, and MSA-C groups, but abnormal in PD, MSA-P, PSP, and DLB groups. No difference was found in regional uptake on early phase images among normal DAT binding groups, except in the MSA-C group. Abnormal DAT binding groups showed different regional uptake pattern on early phase images compared with PD in SPM analysis (FDR< 0.05). When discriminating APD from PD, visual interpretation of the early phase image showed high diagnostic sensitivity and specificity (75.4 % and 100 %, respectively). Regarding the ability to distinguish specific APD, sensitivities were 81 % for MSA-P, 77 % for MSA-C, 23 % for PSP, and 54.5 % for DLB. Conclusions Dual-phase F-18 FP-CIT PET imaging is useful in demonstrating striatal DAT loss in neurodegenerative parkinsonism, and also in differentiating APD, particularly MSA, from PD.