A variety of engineered nanomaterials, such as carbon black, fumed silica and tinania, are produced in flame aerosol synthesis as nanoparticle agglomerates. Other important sources of nanoparticle agglomerates include the soot particles generated from the burning of biomass and diesel fuel. Particles formed in these high-temperature processes are commonly found to grow from nearly-spherical primary particles that are usually tens of nanometers or smaller into fractal-like agglomerates that can be microns in size or larger. This change in particle morphology has profound implications on particle properties, including light scattering, surface chemistry, transport, and potential health effects. The time and labor expenses of offline electron microscopy inhibit its application in situations, such as quality monitoring for nanomaterial manufacturing, where fast measurement of agglomerate structure is required. Therefore, an online characterization tool for the structure of nanoparticle agglomerates is highly desirable. Moreover, real-time information of airborne agglomerate mass concentration is of interest to both the nanotoxicologists and the diesel engine industry. It was found that lower mass dose of nanoparticles is needed for them to have the same toxicity as particles of micron size or larger due to the increased active surface area of the former. In addition, the increasingly stringent environmental regulations call for cleaner diesel engines and it is difficult to use the gravimetric filter method to measure very low mass concentrations of diesel soot emissions. Thus, advances in nano environmental health and safety (nanoEHS) study require a sensitive instrument that can measure low levels of agglomerate mass concentration. With the aid of a newly developed instrument, Universal Nanoparticle Analyzer (UNPA), we conducted online structural characterization and real-time mass measurements for metallic nanoparticle agglomerates generated by spark discharge and diesel soot aggregates. The instrument uses mobility classification in conjunction with measurement of unipolar charging properties to extract information about primary particle size and agglomerate compactness. Reasonable agreement was found between the primary particle sizes measured by UNPA and transmission electron microscope (TEM). Additionally, the instrument was able to detect the change in morphology of metallic nanoparticle agglomerates due to sintering. Based on the agglomerate number distribution from a mobility scan, the UNPA calculates the agglomerate mass distribution using mobility and charging models for loose ideal agglomerates. Parallel measurements of the mass concentration were performed for the loose agglomerates in our study (i.e. metallic agglomerates and diesel soot aggregates without treatment after production) using filter collection and UNPA. Agreement between the instrument-based and the filter-based mass concentrations is good in the case of loose silver agglomerates and reasonable for diesel soot aggregates.