Transport and physical/chemical properties of nanoparticle agglomerates depend on primary particle size and agglomerate structure (size, fractal dimension, and dynamic shape factor). This research reports on in situ techniques for measuring such properties. Nanoparticle agglomerates of silica were generated by oxidizing hexamethyldisiloxane in a methane/oxygen diffusion flame. Upon leaving the flame, agglomerates of known electrical mobility size were selected with a differential mobility analyzer (DMA), and their mass was measured with an aerosol particle mass analyzer (APM), resulting in their mass fractal dimension, D(f), and dynamic shape factor, chi. Scanning and transmission electron microscopy (SEM/TEM) images were used to determine primary particle diameter and to qualitatively investigate agglomerate morphology. The DMA-APM measurements were reproducible within 5%, as determined by multiple measurements on different days under the same flame conditions. The effects of flame process variables (oxygen flow rate and mass production rate) on particle characteristics (D(f), and chi) were determined. All generated particles were fractal-like agglomerates with average primary particle diameters of 12-93 nm and D(f) = 1.7-2.4. Increasing the oxygen flow rate decreased primary particle size and D(f), while it increased chi. Increasing the production rate increased the agglomerate and primary particle sizes, and decreased chi without affecting D(f). The effects of oxygen flow rate and particle production rate on primary particle size reported here are in agreement with ex situ measurements in the literature, while the effect of process variables on agglomerate shape (chi) is demonstrated for the first time to our knowledge.