The principles and applications of time-of-flight mass spectrometry involving instruments with independent (orthogonal) axes for ion generation and mass analysis are reviewed. This approach, generally referred to as orthogonal acceleration time-of-flight mass spectrometry, has proved particularly advantageous for the combination of continuous ionization sources with time-of-flight mass spectrometry. The history of the technique is briefly discussed along with the instrumental principles pertaining to all the stages of the instrumentation from ion source to detector. The applications of commercial and customized instruments are discussed for several ionization methods including electrospray, matrix assisted laser desorption/ionization, electron ionization, and plasma ionization.