The management and spatial-temporal integration of LiDAR data from different sensors and platforms has been impeded by a lack of generic open source tools and standards. This paper presents a new generic file format description (sorted pulse data; SPD) for the storage and processing of airborne and terrestrial LiDAR data. The format is designed specifically to support both traditional discrete return and waveform data, using a pulse (rather than point) based data model. The SPD format also supports 2D spatial indexing of the pulses, where pulses can be referenced using cartesian, spherical, polar or scan geometry coordinate systems and projections. These indexes can be used to significantly speed up data processing whilst allowing the data to be appropriately projected and are particularly useful when analysing and interpreting TLS data. The format is defined within a HDF5 file, which provides a number of benefits including broad support across a wide range of platforms and architectures and support for file compression. An implementation of the format is available within the open source sorted pulse data software library (SPDLib; http://www.spdlib.org).