Nuclear medicine imaging techniques like positron emission tomography (PET) and single-photon emission computed tomography (SPECT) apply radiolabeled drugs that bind selectively to specific neurotransmitter receptors and transporters such as the serotonin transporter (SERT) in the living human brain. They can help overcome certain limitations of postmortem, platelet and genetic studies of the SERT. This review compares the outcome of those studies with recent neuroimaging findings. The first part of this review deals with the choice of radioligands used to quantify SERT distribution in the human brain. The second part summarizes studies performed to understand the normal physiology of the serotonergic system. Selective serotonin reuptake inhibitors (SSRIs), used to treat a wide range of neuropsychiatric disorders with emotional instability and behavioral control deficits, compete with SERT radioligands and have been investigated in pharmacological PET and SPECT studies in healthy volunteers and patients. Part three reviews SERT imaging studies in patients, which have meanwhile been performed in most disorders that benefit from SSRI treatment. It is hypothesized that serotonin deficits and neuropsychiatric symptoms are linked by the inhibition of involuntary emotional reactions to external and internal stimuli. This could explain, why the consistency of many SERT neuroimaging findings is low, and may help develop individual treatment strategies in therapy-nonresponsive cases and to engineer new drugs for the therapy of neuropsychiatric disorders.