This review introduces advances in clinical and pre-clinical single photon emission computed tomography (SPECT) and positron emission tomography (PET) providing noninvasive functional images of biological processes. Development of new collimation techniques such as multi-pinhole and slit-slat collimators permits the improvement of system spatial resolution and sensitivity of SPECT. Application specific SPECT systems using smaller and compact solid-state detector have been customized for myocardial perfusion imaging with higher performance. Combined SPECT/CT providing improved diagnostic and functional capabilities has been introduced. Advances in PET and CT instrumentation have been incorporated in the PET/CT design that provide the metabolic information from PET superimposed on the anatomic information from CT. Improvements in the sensitivity of PET have achieved by the fully 3D acquisition with no septa and the extension of axial field-of-view. With the development of faster scintillation crystals and electronics, time-of-flight (TOF) PET is now commercially available allowing the increase in the signal-to-noise ratio by incorporation of TOF information into the PET reconstruction process. Hybrid PET/SPECT/CT systems has become commercially available for molecular imaging in small animal models. The pre-clinical systems have improved spatial resolution using depth-of-interaction measurement and new collimators. The recent works on solid state detector and dual modality nuclear medicine instrumentations incorporating MRI and optical imagers will also be discussed. (Nucl Med Mol Imaging 2008;42(2):98-111)